Within every race or organization there are those who would seek power and create dissent. Perhaps there is a group of mindflayers who we do not know in yet. By capturing the remaining dopplers from BG2 and forcing them to work as sleeper agents, said group could kill both factions without being detected. We destroyed them in BG2, but its implied a few of them survived. A greater doppler can explain why our mindflayer is stronger then those of others. Dopplers can already use psychic abilities to read minds, it would make sense a mind flayer tadpoll would make them stronger. Likewise, dopplers as shapeshifters may be immune to the catamaorphisis.
Its true we are tricked several times. But that may be a by-product of a doppler not knowing they are one, and hence thinking in lines of a humanoid. Humanoids are imperfect and their limitations of the original still pass on to the doppler. It makes sense that one that is experimental, this would apply more to.
Regarding zarial yes, your right. I meant more in the lines that Raphael may want to become a full devil right. We are told he may want them for more power, as his human side is fallible. He already shown to change his looks to one that looks human. Would not surprise me, if the paladins think they are working for zarial, but are not actually. Could maybe argue that Mephalis, would want Zarial gone. For all we know, mephalis may be raphael as he is known for tricking people. Pathfinder did this in wotr as well where mephalis pretends to be a lower lvl devil.
