Well... unless plans are made for major (seriously major) improvements of the "post-Shmitz" parts, then I'll have to second the others here.
I don't mind the flaws/glitches much, apart from the awfully long boss fights, the middle finger waving Doctor and the game breaking Nemesis X theft... but those should definitely get a quick fix, and Shmitz ought to be given his due. That and the Red Tower's "trial and error death traps maze" is pretty much the formula of anti-fun.
If the mod was to be... "continued from scratch", I would reccommend a drastic rethinking of the story's development (we have already discussed this via PM, if you recall, but I don't think you were very fond of my ideas either, considering it "overthinking the matter" if I'm not mistaken).
Certainly not having Curly mandatorily dying would be for the best, especially after all the trouble we went through to save her in the first game.
...aaaaand I read now (in posts made after typing the above) that you're pretty sick of working on JN, so yeah, I guess the bareminimum fix it is then.