I think a clever way to add a little more depth to the gameplay aspect of the game might be to implement a series of different debuffs, restraints or limitations to some NPC's that have to be overcome.
Some of these could be simple resistance to certain types of transformations that require you to research a way to overcome it. Some could be a propensity for a certain type of event to happen no matter what you're doing to the subject, or perhaps a small chance of a completely random effect occurring. Maybe even negative traits that simply lower output if you use the wrong types of experiments on them.
However, I think it would be rather interesting to determine these effects independently of how a subject generates their wants/desires and requests of you. Perhaps even allowing for massive bonuses if you help some poor soul with, say, a shrinking fetish that has traits that prevent you from doing it.
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