An overwhelming number of confusing and conflicting grindy mechanics which dilute the good parts of the game. It's a shame because this is the closest he's been to having an actual plot and story progression. If he insists on sticking to the rpgm leveling and skill system, then he needs to streamline it. Either tie skill acquisition to receiving/doing attacks to a particular body part, or have them learned automatically as you level. It would also tremendously help with balancing which has always been broken in his games.
It's really unclear how you're intended to progress at first. You want to unlock more cutscenes and more areas of the body by spreading the infection. That means creating more cross-breeds, but it really wasn't clear how fighting immune cells, infecting non-hostile cells, impregnating cells or voring cells contributes because none of those actions directly create more cross-breeds. Instead it all boils down to fighting mobs to grind for resources which is awful. If it were me I'd try to tie combat with pathogens and host cells more. First get rid of all non-erotic attacks and skills, and treat HP as just how much arousal damage you can take before losing. We're here for lewds, make everything lewd. Stop making us deal with reapplying arousal. It's miserable.
A great idea would be that your player has to first take in pathogen genetics through making them ejaculate, but because you're a pathogen you can't replicate by yourself, and instead need to insert those genetics into host cells to produce cross-breeds. Further don't just allow any cells/pathogens to receive any kind of fetish attack. Make a rock-paper-scissors system so there's some thinking behind what body part you attack, and it also helps with theming and adds variety to each enemy type. Rather than pure xp grind, have the cross-breeds and huggy acquire skills by receiving genetics through ejaculation with that body part from specific enemies that focus on that region.
Last create a combat system where receiving and applying attacks is a balance. Thematically I'd tie everything back to genetics and breeding. When you take attacks from a specific cell/pathogen they should each apply a specific debuff that causes you more damage/arousal, but also increase your ability to take in their genetics (learn skills & become pregnant/impregnate). This could easily be illustrated with each enemy having a limited number of unique debuffing skills that show on the character sprite when applied. Further these should be the same skills you're learning as you acquire more genetics. Enemy difficulty would mainly be based on how much you need to apply/withstand debuffs before your attacks do significant damage rather than pure level grind.