AA2: better npcs, npcs interact with each other, lots of mods, lots of positions, other males allowed, can play as male or female
Koikatsu: More control during positions, a few set stories, a more varied character editor, a built in scene editor for making your own positions or importing from elsewhere.
personally, I prefer AA2. it has much more replay-ability, and the characters feel more alive and varied. koikatsu is good for 1-2 playthroughs, but I have legit played AA2 for probably a hundred+ hours. being able to play a male or female, student or teacher, different play styles, with different NPCs? hard to beat. also a lot of games use koikatsu's engine to make their CGs. if koikatsu were a tag on here, it would probably have somewhere between 5-10% of all games. not sure if that's a positive or negative for playing koikatsu itself, but its really noticeable and you won't be able to take that back.
also AA2 is apparently from the far future. so its better