My issues with Project: M are threefold:
1. Recovery is too easy
Reminiscent of Brawl, recoveries have been made to ensure safe, easy recovery in a huge number of situations. Every P:M specific character (i.e. a character not in Melee) has a fantastic recovery (obviously exaggeration, I know a few who don't), and more importantly an easy recovery. I am not a fan of the idea that falling offstage is not a huge disadvantage. For characters like Ivysaur, Charizard, Sonic, and others (whom I wont bother to name), recovery is a no-brainer. It takes no skill, there is no risk; there is only risk for the edgeguarder if they try to kill them.
2. Combos are semi-auto
Much in the way of N64, throws=death, which is fine, but instead of a simple throw for a kill, Project: M opts to create the illusion of a combo by making throws lead into guaranteed kill followups. So not only does a throw at high percent equal a kill, but now you can be killed off of a throw even lower because the throw adds percent for the guaranteed finisher. Also, eliminating the power of SDI is, for me, a negative, making combos, again, easier.
3. Characters are designed to be too powerful / simple
Instead of giving each character good tools, and allowing for player innovation, each character has moves for specific instances, where it is undoubtedly the best option.
Ex: Spacie recovering against Marth in Melee : once spacie is forced to go for ledge, can use dtilt, fair, fsmash, dair, bair, neutral b, or nair depending on situation.
Spacie recovering against Squirtle in P:M : once spacie is forced to go for ledge, bubble.
Spacie recovering against Lucario in P:M : Aura Bomb (if you have it, but when don't you have it, you get it from hitting SHIELDS as well as players)
There are nigh-innumerable examples of this phenomenon, both in combos and edgeguarding.
Instead of opting for better core tools, the developers gave each character moves for each situation.
3 and a half: NO LIGHTSHIELD
3 and three quarters: SONIC EXISTS