I know nothing about game programming but for a game with this much content, I feel like it would be better to have broken it up into volumes.
Instead of mashing everybody into the same game and trying to update the same content over and over, why not just have the game with 3-5 girls?
Then in "Volume 2" you introduce 3-5 new girls and a new mission in the same city/setting from the first game, if you want to see the girls from Volume 1 you go back and play that game, Volume 2 could take place in Metropolis like the first, you just have the new 3-5 girls taking the place of the original 3-5, different scenarios, different missions to accomplish, stuff like that. Also, as you level up your stats you can unlock a save code which when entered in the next volume/release of the game, lets you carry over your stats from the previous game.
I would flip flop the settings between Metropolis/Gotham, and then maybe Vol 3 would be a setting in the Marvel universe with 3-5 girls.
Also, I would want to make it so that you could export all images/scenes you unlock to your hardrive. Basically, I would have designed this game like one of those collected graphic novel books. I feel like from here on out, the game is just going to get more and more broken as more content is added and starts to conflict with old data.