I love this topic, though I probably wont add much not keeping notes and posting a mega-post for the 5 pages read.
I do very much agree the KOTOResque (which I have a lot of experience with ;)) idea clashed a lot where the plot gives gray an option but gameplay-wise you get heavily punished for it (locking content even).
D:OS also used a similar system I hated, the perk one. Never liked it at all. It literally forces users to powerplay... and... that was all it did. It was a pretty poor counter-productive element added to D:OS that had no place and heavily detracted from roleplaying (I picked an option I liked, now the perks are +1/+1, I get no bonus at all... greeeeeat). Not to mention how pretty much all were skifted to one side in the first place with option A having a great bonus and option B improving a stat that was worthless.
I already put my thoughts on killing, XP and such discussed early on in another new topic.
And I agree much can be learned from Planescape: Torment and Deus Ex in rewards system, even if they are first-person semi-FPS. There is no way their system cannot be implemented in an isometric system. Especially one story-centered as D:OS2 is shaping up to be.
