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The change of environmental mood is a very nice idea indeed. Having mudokons running in the background and spaying graffiti in RF would make the player more aware of the impact his positive actions have on oddworld.
But personally I would keep the puzzles unaffected. 
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Agreed. Also, the Mudokons emotionally affected by Abe's quarma should say something more meaningful than the normal sadness "umm" and the anger "nyarrrg" (How the hell would you transcribe it?) so the player would know they're specifically angered or saddened by Abe's actions. For example, angry Mudokons could say things like "I hate you", "you suck" or, if the casualties count justifies it, "you terrorist", and depressed Mudokons could say things like "I'm doomed" or, if the casualties count justifies it, "you killed my buddies". Of course don't make these too obvious or else they'll suck. :P
Also about Mudokon emotions, make them change less sharpy. E.g. in AE a furious Mudokon who have just tried to kill you suddenly becomes all friendly and cheerful after a plain "sorry". Make these keep a slightly angry/sad tone for a few minutes before reverting to the default voice.