I agree that the game is good but falls too short compared to the first two.
The puzzles were good as well as the technical aspects but the story was full of questinable decisions, but not because it tries to answer everything, but stupid things and asspulls.
My gripe is that ZTD converted smart characters into complete idiots.
Sigma, Phi and Jumpei aren't even half as smart as they were in the previous games. This is even more aggravating in the case of Sigma and Phi since they were on a mission but did nothing about it.
Also wasn't Sigma supposed to be his young self most of the time? If I remember VLR plot correctly they were preparing Sigma and Phi to go to the incident knowing just enough to not know how things happened so they can change the outcome schrodinger cat style, but Sigma was (AFAIK) almost always his old self.
Things happened too conveniently too, Carlos didn't knew he could jump and mastered it on a few hours while Sigma and Phi had to spend a whole nonary game to do it. That also applies to Jumpei and Akane that suddenly and without any reason were able to jump.
Delta's intentions were so "complex" that not even Uchikoshi knew them apparently and are never explained.
I'm sure there were some plot holes too but I can't remember anymore and if I could I'm sure I could go on and on.