Mewtwo's nair is a lot better than you guys think, it's definitely useable in neutral, it's pretty hard to punish, and the hitbox is deceptively large, especially on start-up against taller characters (partially owing to Mewtwo's ability to move during the move)
Point by point.:
Frame 7 is really not that bad, you just can't use it in absolute CQC. You can can control your momentum during the move very well, and as long as you drift into opponents you can get punishes constantly using OOS nair against any number of mispaced aerial approaches (which mewtwo tends to force via the d-tilt/fair/sball wall of frustration). For example, drift into a Diddy fair OOS and you'll beat it -- something I hope Mewtwo players start doing in this match-up.
Secondly, Nair has a much bigger hitbox than people think and you can absolutely use it in neutral. As long as you're playing with tilt-stick you can control the direction you drift afterwards -- and it's very safe. You can't throw it out full-screen, but it beats a lot of options in CQC if you're around Mewtwo's jab-range, it combos into all kinds of things, and if they shield it you're fine since they can't challenge between hits and you can just drift through/fast-fall and pick a defensive option. Abadango does this all the time, and people still fail to punish him for it -- because it's actually really difficult (impossible for most characters).
The move is very easy to combo out of as long as you know your percents. The mistake most people make is trying to predict which side the enemy will pop out of, but really you can just react. In certain situations you can control the pop-out as well (full hop nair, ff-6 hit nair from the front or RAR) with specific DI. Sure it takes a while to learn all of this, but it's not as bad as people think.
Basically just nair, stay vertical, DI away in a direction at the apex of your short hop and the enemy will either land right in front of you or right behind you (sheik you can get in front of you 100%, some other characters will end up behind you -- but it's not random). Then you can footstool disable, turn-around d-tilt, grab, and so many other things...
It's a really good move, people who think it's bad are wrong or must be throwing it out at the wrong range.