I just hope that if we chose Nova the story will actually change and we will join Crescent and become their allies. Too may hack I've played advertise the feature of joining their respective evil team as an option, but fall through on this aspect.
Oh, and don't worry about not increasing the level cap in episode 4. Don't let this problem allow you to dampen your ambition and shorten the game's length. After all, you can always increase the level cap to exceed 100, so that's not an issue.
Other than these problems you're doing a great job on delivering on your ambitious game. Especially for a first time like yourself, you clearly have talent.