I kind of think that the infection mechanic could use a little more meat. Heh, meat...
Anyway, more than one counter. A counter for your specific, currently active infection and an over-all counter for the nanite infection level. The more often you're infected, the higher your nanite infestation gets, the more susceptible to further and more dramatic transformations you become. Maybe there could be healing benefits to higher infestation levels while your mind becomes more susceptible to those rapid transformations as well.
More infection areas would be really cool as well, head, torso, butt, etc. could be divided up to cover a lot more parts of the body. It could also allow for more variation of the various mutations, like a butch girl-bunny, or a sissy cheerleader, or grizzly. There's a lot of potential in a more nuanced system of transformations, instead of trying to cram more and more transformations in the game, why not expand each one more completely to fulfil the game settings (male, female, shemale, fem-boy, butch, dom, sub whatever). The mutations could be more than "This kind of monster is a dominant shemale, this kind of monster is a submissive female". You have a lot more potential when you're making your own engine to tailor the PC to the player than you do in the old text format.
Is that all very complicated? Maybe, I don't know, but that's not my problem!
Most of the numbers for the entire game can be enhanced as well, libido can be a more nuanced system. Ditto for Fertility and Virility, semen volumes, ovum production. Even saliva, and body capacities for un-birth or whatever can be given a more solid and transparent numerical base.