Hi Entheo,
Hope you don't mind if I jump in?
Pluto in the 3rd house, Mercury in Scorpio, or Scorpio ruling the third house. My intuition tells me nothing, archetypically speaking, Well, appears to me your intuition needs a bit of improvement...that’s not a judgment just a simple observation hope you are able to take it objectively...

Well, maybe you happen to have sag on the 6th cusp? That would point to the above in general....so would 3rd Pluto pointing to 9th house....anyhow, talking about possible sag on the 6th, it is really important to understand how different it is if let say jup would be in the 6th ...that in essence would mean that the soul is consciously DENYING the truth about something...what that maybe the whole chart would need to be examined to see what and why that is the case....for there can be infinite reasons of course. So a sag 6th cusp in itself just points to the need of IMPROVING the intuitive faculty and jup needs to be examined to see why, how etc. Of course the bottomline here would be the fact that the mental faculty as such (i.e. gemini, in that case the egocentric mental faculty, impact via the immediate environment etc. would be the 12th cusp so something needs to be culminated about that for it lead to some degree of confusion/illusion)
Again that in itself is different than jup in the 6th: denying the truth about something in some ways, for some reason...
The third scenario in this aspect would be virgo jup in some house. This will be highly dependent on the house placement to see what it relates to: but the bottomline will be the fact that the person is doubting/denying their OWN intuitive knowledge probably because they feel their intuitive faculty their perception of the truth is "inferior" somehow. But again the whole chart would need to be examined to see the reason and find the answers. So this is another example of the same you asked....how one archetype plays out differently....
As for your original question the same is true: there is WHOLE LOT of difference between Pluto in the 3rd house, Mercury in Scorpio, or Scorpio on third house. Pluto in the 3rd simply points to the fact that the soul havae been developing for a long long time its mental faculty. Depending on the sign on the 3rd cusp AND the sign pluto is actually in (for it may be a different sign than the cusp and that's very important for in that case, the 3rd house in itself STILL will have the nature that the cusp signifies but it will then LEAD to the next sign that pluto is in. Yet the overall 3rd house issue, including but NOT exclusive to the mental faculty (immediate environment, experiences + how they are processed mentally etc.) all of this will be essentially originate from and rooted in the sign of the 3rd cusp.
Anyway, so whatever the case maybe a 3rd house pluto will always pay attention to it's immediate environment, physical and mental and will try to somehow affect and penetrate (pluto) into the whatever bottomline (that the soul perceives as bottomline) of that immediate environment and the mentality behind it. It will have loads of experience from past lives how to do that, how to communicate how to be "intellectual" so to speak. The soul in this case would obviously have a ppp in the 9th house which would point to move away froom the mentally structured and logically built "opinions" which maybe very well built, however may not embrace the essence of what is "true". That's what the ppp. points to, truths are not possible to mentally 'structure' or 'logically create' there is a limitation of the egocentric mental faculty; of course the real knowledge the truth can only be REALISED. For they are already "out there" they can be only perceived intuitively. They have nothing to do with "logic" or egocentric "intellect" or "good communication skills" to "sell them" so to speak. However within a 3rd house pluto these will be the skills the soul developed and the need will point to fill in and balance the existing skills with the value of the actual truths. 9th house.
Anyhow, mercury in scorpio will HIGHLY depend on the house placement and of course PLUTO'S PLACEMENT.
Mercury in scorpio will always point to the fact that the soul is attempting to think and communicate in a way that SERVES THE SOUL'S UNDERLYING INTENTIONS.
So in actual reality this can be ANYTHING relative to THE NATURE OF THE GIVEN SOUL.
I.e. it can point to someone who is incredibly secretive and deceptive (IF THAT'S what the soul intends!) or can point to someone who is communicating from the very depth of their soul. All this depends on the soul itself: it can be unravelled from looking at pluto and the WHOLE chart of course.
So truth is that no 'general description' can ever explain mercury in scorpio because of the above...it DEPENDS on the intentions, agendas and deepest motivations of the soul. One is for sure; the INTENTION whatever that may be is coming RIGHT FROM THE DEPTH of the SOUL. That's the only sure thing. WHAT THAT MEAN is of course the real question.
To unravel this the first thing needs to be considered is the HOUSE placement; for communication/thought process etc. etc. so all mercury correlations will be implemented AND lived according to the particular house placement. (and lets not forget that virgo is also ruled by mercury, so THAT will also be ruled by the scorp. mercury next to gemini. So again it is extremely important to understand that archetypes are NOT eqaul when they manifest in any chart. The so called "nuances" are the very heart of the actual reality of the soul so the very heart of the chart itself.)
As for scorp. ruling the 3rd house, you have a different scenario here, it certainly won't rule virgo we aren't talking about mercury we only talking about the 3rd house: all immediate experiences, the person's immediate environment, physical and mental, events observations etc. etc. will be perceived very very deeply and the mental and EMOTIONAL (scorpio) processes that this environmental impact creates will also reach deeply into the soul.
Meaning what happens in the person's immediate physical/mental environment can be deeply metamorphosizing, OR entrapping, deeply deceptive OR both. It will of course be ruled by pluto, so again the house and sign placement of pluto will give the cues as what could be the reason for this what's the limitaiton in the natal pluto which created the entrappment at the first place, how, why etc. etc....maybe the person needs to realise something about it's own intentions relative to its immediate environment, or maybe it needs to become aware of the ENVIRONMENT's intention OR BOTH......it all depends...again it can NOT be known just by this one aspect of a chart...
What is for sure is that the 3rd house issues (siblings for example, or the general environment etc. etc.) somehow in some ways very very intense, and creating some form of entrapment for the soul in one way or another....wherever scorpio itself falls to our chart there is some form of entrapment in something and there is the area of life which needs to be metamorphosed via METAMORPHOSING the natal pluto limiations...that will always directly impact on the scorpio area of the chart....
This can be ANYTHING....one's own beliefs, if scorp falls onto the 12 house for example, or one's own perception of what's wrong with it's soul, if scorp. falls in the 6th, or one's way of creating relationships if falls on the 7th, or one's own way of self actualization if falls in the 5th, one's own way of expressing/sharing oneself with the world if it is 1st house, and so on and on.........how and exactly what and why needs to be metamorphosized cannot be said until the whole chart is examined thoroughly.... Again the whole chart! THERE IS NO GENERAL way of saying "this or that" is the meaning...the ACTUAL MEANING in each case can be very very different.
Let me give you a few example how this can play out: let say a scopr. mercury is in the first house ruled by a 9th pluto. This in general would correlate to a soul who is utterly honest and trying to communicate the intuitive truths that it perceives from its deepest soul level. This would be a person who instinctively shows its soul in its depth, which in itself can create many wounds for that soul without the person knowing why.... It will be instinctively intense and will come without forethought from the very depth of its soul with an intention to express and teach the truths that it intuitively perceives. The 'entrapment' in this case will be the very way how it expresses itself which will be defined by the 9th pluto, it will be instinctively repelled by everything that isn't totaly honest and truthful AND it will instinctively show it with intensity. This will be the reason for many souls who are untruthful for whatever reasons to REACT to the soul with hatred an anger and undermining intentions. So the soul will be wounded via it's own way of expressing itself intensely right from the soul level with such honesty. Even that can cause problems within our paradoxical human reality. It will point to the need of metamorphosing above the previous limitations as how to express oneself and what to show and to whom about it's soul.
Now let say a scopr. mercury is in the 5th house and let say it is ruled by a 3rd house pluto: this will be utterly different for there will be a soul who places importance on the egocentric mental processes (3rd pluto) which will be communicated in a 5th house fashion: it will revolve around the intention of a 3rd pluto soul: that is about the egocentric intellectual "virtues" and communication in general, and of course it won't be instictive. I will be structured around some sort of logic (3rd house) which will be implemented in a 5th house way, revolving around self actualisation. The soul would be highly dependent on the immediate environment (3rd house) for feedback (5th house) and this will reflect a need to be "acknowledged" 5th house for its soul's intellectual abilities. This in intself would have noting to do with honesty it would have to do with what the soul thinks it "works" in order to be in the center of attention (5th house) This will be the area of the "entrapment". The soul's own way of actualising itself would be the very issue which needs to be evolved beyond. In this case the entrapment would point to the mental, intellectual processes that are the underlying intention for the scorpio entrapment: i.e. there will be some level of double facetedness something that is done just to sound clever so to speak for the intention of having the feedback having the 5th house "centre role". That very role creates the entrapment for the soul in this scenario.
The possible problems can be: the soul is too caught up in it's own mental processes, its own opinions and creates all kinds of "logics" sometimes contradictory even to iteself just to penetrate into the it's whatever immediate environment and communicate it's opinions in a way that it can in one way or another bring the 5th house reality alive: being the center of attention and having the feedback of how "wonderful I am". With the 3rd pluto it will translate to "how brillianat I am"
This entrapment will be difficult to metamorphose for the person with a 3rd pluto and 5th scorpio mercury will be able to penetrate into the environment and have learned how to manipulate the "audience" so to speak so it will be very easy to continue the old way instead of making any effor to metamorphosing the limitation. The need for it occurs inwardly within the soul, while at the same time the soul is highly focused outwardly. (3rd and 5th house)
The self centeredness a soul with this pattern manifest may be innocently deceptive (depending on the WHOLE CHART!) or maybe intentionally very deceptive. If let say that that 3rd pluto happen to fall in libra it would suggest a soul who learned how to be ‘likeable’ via it’s communication skills, and that knowledge could create a very deceptive 5th scorp. mercury; people who hear him think the soul give what they need, yet in essence the soul is serving it’s own 3rd house based 5th scorpio needs via mercury there. (to be in the centre of attention)
Or if let say pluto falls in virgo in the 3rd relatiave to 5th scorp. mercury it can correlate to a soul who is judgmental of others and may implement it’s 5th house scopr. needs via putting others down and elevating itself this way. This would be a result of a highly skilled communication technique behind which is a thought process to find the weakest link in anybody else's “logic” and undermine it. Or lets say if the 3rd house cusp is virgo but pluto is in libra within that 3rd the soul may be able to do the later in a way that in the same time will appeal to it's immediate environment and may use it's libra "charm" as to deny the original 3rd house intention to undermine others, so as to gain the 5th house scopr. feedback "how brilliant I am".
Of course all this depends on the overall patterns of the whole chart. These are just examples of the possible implictions as what can be the motivations, agendas and actual intentions of the soul/pluto that rules scorp. mercury.
For example if pluto would be in the 4th instead of the 3rd and ruling the same 5th scorp. mercury we have a totally different underlying issue: the soul is trying to emotionally relate to itself trying to define it’s self image which has nothing to do with 3rd house issues i.e. immediate environment, higly developed communications skills and need to be acknowledge for mental issues: in this case the soul's intention would be around emotional issues, the soul would be intenting to actualise itself and have positive feedback via communicating EMOTIONALLY and passing on emotional soul- content and not intellectual content. This would create a toally different picture for the soul would come from a totally different intention. ...again everything depends on the WHOLE chart and within that the INTENTION of the soul....
Anyhow, the above are only GENERAL possibilities (so please do not take them as absolute!:-) they are just to demonstrate the EXTREME difference within certain symbols as we apply it within a chart....just to show you how utterly different the actual MEANING can be....
So in summary, nothing is farther from the truth than 3rd house pluto, scorpio 3rd house and mercury in scorpio. “means the same”....
Hope this helps?
Blessings,
Lia