I find Baroque to be a far better comeback mechanic than X-Factor TBPH. Granted, I haven't actually played MvC3 yet, but I do know a lot about the mechanic via what I've read on the web as well as stuff I've heard from my friends. I'm not really a fan of the comeback mechanic being an "on switch", so to speak. With stuff like Baroque, you had to actually plan what you were going to do ahead of time, and there's more of a risk to it. With X-Factor it's more of a signal for your opponent to play keep-away until it runs out, though it can be cancelled into for big damage. Really the whole X-Factor thing just doesn't seem necessary as a whole, and to boot it doesn't even seem fresh or interesting.
In a fighter there's less of a need of a comeback mechanism than in other genres, because both players have access to the same tools no matter how much of a life lead there is, though without teammates in the Vs. series you obviously lack assists and the like. Of course, Phoenix would be the odd exception to the rule as she actually grows in power when she's on the losing end.
Also, on environments, I'm aware that Brawl's tournament style allows for some more stage flexability than Melee's did, but there's still a large variety of environments that don't get safely tucked behind a "banned curtain" in general play. Also, much of the stage selection of Brawl's tournament play is a result of Brawl's unimaginative level selection and over-use of large flat aeras (Smashville, Yoshi's Island Brawl, etc.). There are a few more varied levels that are considered permissible, but for every Pokemon Stadium Melee that's allowed, there's plenty more banned Green Hill Zones where it came from. It's a wider niche than the Melee tournaments of yester-year, but still a niche, and one which the gaming populace as a whole is in no way bound by.
Really, I kind of wish Nintendo was a little better at designing stages that are both fun while at the same time being innovative and balanced. A lot stages on the banned list I don't really like in the first place. Green Hill, for example, just feels really cramped to me, and you can pretty much just camp in front of the bumpers all day if you really want to. I think Smash 64 had the best designs, as while the number was small, they all felt unique and fun yet remained balanced as well. Hyrule Temple 64 is still one of my favorite stages in the series, as it had a varied terrain, that fun little tunnel, and those tornadoes to shake things up a bit (bad pun, sorry).
Thankfully, with Brawl you can replace the stages you don't like with downloadable ones that are often more interesting. Obviously this isn't a tourney move, but when playing with friends it allows a wider variety of stages to be used since you no longer have to deal with the stages that everyone in your group hates (that means you, Rumble Falls). It wouldn't be a bad idea for tourneys to simply overwite the banned stages with better versions, as there's a lot of creative and useful stuff
out there.