The Common Philosophy Schema (we are all but memory and dust..):
Posit a common philisophical belief of the villain; something very common sensical but abstruse enough to be unusual and preferrably fatalistic. Have seedlings utter this belief before fighting, dying or doing something counter to the PCs best interests. The PCs will probably think they are dealing with a cult or somesuch at first.
PC: "Barkeep; a frosty mug with your darkest to the brim for each of us." Turns to fellow party member known for intelligence; "So what was the deal with that crazy street thug that attacked us? He was talkin' some serious nonsense...what was it again? 'Memory and Dream, Thought and Deed ....and what was it a again?"
Tavern Keeper: "I believe it goes 'Memory and Dream, Thought and Deed, Idea and Seed'. Its a common saying around here. Here's your drinks noble sirs."; as the seeded Tavern Keeper slides poisoned beers to the PC's....
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The Hydra Schema (cut off one head...etc):
Have a wide variety of seedlings address the group, using the plural 'We'. In this scenario the mystery isnt to realize that the subjects are mind-dupes but instead to figure out what kind of bizarre fanatical cult the group has stumbled upon. It hides the true plot in plain sight by making it look like something else.
7 year old girl: "We see you havent decided to stop meddling yet. Youre wasting your time; we are everywhere; we see everything. Your thoughts are transparent to us, your attempts to stop us laughable. Leave, or become one with us. Your doom is upon you for we are Many, while you are few."
hero: "What the #$#@?!!!"
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BTW: Since the subjects of Mind Seed diverge along thier own path once they are seeded, the subjects would have independence, but any Psion of high enough level to Seed them in the first place should have another telepathic power with which to coerce his mind-clones.
Otherwise, the subjects would be independant operators. Also, depending on the personality of the Psion, his seedlings may vie with him for control if he doesnt coerce them in some fashion.
If I were to pull this off, I would try to lead the players to the belief that they were dealing with a Cult of Erythnul (the Many), as I run a Greyhawk campaign. I would leave red herring type clues to mislead them as long as possible and maintain the mystery.
Baring that, I might try something like a Fight Club spin, where the Psion was trying to pull off something like the overthrow of a government via his army of mind-seeded minions and the PCs just sort of stumbled into it from the flanks. To add to the confusion, the government might well be corrupt and oppressive and there are a goodly number of non-mindseeded people in this organization, many of whom are actually good people working to cast off a tyrannical regime (what does Tyler Durden look like!?!). Thus the moral quandry is introduced to the mix, as the Psion's organization is not necessarily all bad, but the methods the Psion is using are.
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All the BLAH BLAH BLAH aside, I would be interested in knowing how you use the Mind Seed concept and how it works out.....