It is possible that the guy with the numerous highlight clips displaying his grab combo prowess and a grab combo named after him is renowned for his competence with grab combos.
I'm not sure Fly has an explicitly better neutral game. I think evaluating their neutral games against one another is hard because they play as differently as one possibly can with their character. It would be like comparing Mango and Jman.
In regards to placing Chu above them, it's also worth noting that M2K has lost his last sets to Fly and Wobbles whereas he beat Chu. Barely, perhaps, but a win's a win. I understand there were weird circumstances at APEX 2012 and his set vs Wobbles at Genesis 2 was pools, though (and pools matches are sometimes played in a funny way if you know you're gonna make it out anyway).
I think Chu excels against certain kinds of players in general. I don't think he's better than Fly or Wobbles, but he played well that day, got a bit of a buff from HBox agreeing to go back to FD (or was DSR off? Whatever), and I think he's generally good against people that play patiently. I think years of being camped by Marth fairs and crap as ICs has taught him a lot about how to time & space movement and attacks around people's defenses (and minimize risk while doing so), which is basically godsend against some of the players he had to play that day. Jman killing himself also helped (although he might have won that one anyway). I don't think he had to play Hax either (who I think would have trounced him).
I find the old school pros (with a few exceptions) tend to be kind of meh against Falco and Falcon.