I really LOVED this game. Here is what I found:
1. If able to keep Nagisa alive for all the game, the ending where he can't leave is still there, meaning he must of "died" before meeting Kokichi and Gonta.
2. If you go past Tsumugi in the sewers ( NOT REVIVING HER ) you can actually climb the ladder, and walk on the wall anywhere, which is pretty funny.
Current goal is to get my team to lvl 99. Wish me luck? :D