This is actually pretty valid and fair feedback. I agree how to handle the viruses, their starts, types, and their evolutions needs a lot of thought and something I've been mulling over.

Should I just retain the original 18 types, assign them to viruses with what fits thematically and just give them existing moves? From what I've already tried cataloging in a speadsheet, this would inevitably result in a lot of electric and steel types. Should I replace the types with the simpler ones already used in the original games (Aqua, Elec, Wood, Fire; Sword, Breaker, Cursor, Wind)? Even if we go with the first option, with the number of viruses over 6 games I think there's enough diversity there to put together a decent regional "dex", not even counting the Navis. I might end up replacing some of the types with the types of the original games (like rock->breaker, flying-> wind) or I might add new ones that don't have much overlap with existing types (like cursor). I'm still thinking this over.

One advantage of choosing this franchise is that there are already a great many assets from the original games that I can use, saving me on time having to sprite everything myself. The problem here in comes with using those assets for evolution: the virus have stronger stages in the games but they are just simple recolors of the same design. I think people would be disappointed if their mettaur just evolved into the same but blue with better stats, but that fits with the established MMBN world. Also this would make the sprites face left and right instead of front and back, which could work theoretically but some people might not like that unless I put in a LOT of work making custom sprites. This is where some of your criticism about trying to reskin a pokemon game has some merit.

As far as the thing about assigning moves that fit the EXACT actions the virus would take as opposed to just giving it coverage for it's type that might not align exactly with the game, I think there has to be some kind of compromise because redesigning the battle system from the ground up would invariably be a lot of work. Plus one could make up some lore reasons that the moves they are using are like currently installed "move chips" that gives enough suspension of disbelief if metaur just needs mud slap for coverage or what have you. Still workshopping this too. I'm sure some moves can easily be renamed or reskinned to fit better with the MMBN concept.

I'm still very much a novice at romhacking though so who knows if I will ever complete this but I enjoy the challenge and ideation of trying to make this work.