What tends to happen at higher levels of TvC is that teams like Karas/Ryu or Zero/Alex simply shove you into the corner, and if you do absolutely anything to try to escape, they will simply Mega Crash you right back into the corner. You can even mega crash in response to a defensive mega crash and come out on top because you did yours second. There are even setups where certain characters get a full combo from hitting you with a mega crash into the corner, meaning they get damage, plus most of the meter back, and you are still defending in the corner.
Baroque tended to make this even worse, by giving the approaching attacker a way to get even more super meter (all you needed was a sliver of red health, the actual amount of red tended to be trivial).
Okay, I understand the gripe for a mechanic that's meant to be defensive, it can also be used as an offensive tool. Something that wasn't intended by the developer. Like you said, certain characters have setups, Karas and Zero are the main offenders because those two are heavily reliant on Baroque or resets to do damage and their Hypers - except for Lv.3 - are ass. It also helps that those have some of the best meter-building combos in the game. So, meter to them is just used for Mega Crash, Cross Counter, or Air Raid on the odd occasion for the last two. If that's the case, if you're sitting on a stock of four or five bars, what are you going to use it on?
For the other portions of the cast, they only Mega Crash because they don't want to get combo'd and want corner control; converting it into a combo is just extra and they at best gain one-and-half meters, outside of specific cases (some of them also are distance specific, and you need to be on the ball to confirm from). And sure, you can Baroque to ease the damage scaling and gain more meter, but again, that's a character specific situation where you have to weigh the pros and cons on doing so. I've seen a number of Yatterman-1 players, who rarely Baroque on a Mega Crash and just use it for purely corner control because they'd rather save the Baroque for a reset or conversion.
So, while there are problems with Mega Crash. It's not inherently the mechanic itself is the main problem, just that a handful of characters tend to abuse it more than others - mainly Zero. Besides, Tatsunoko is a very fast paced game. Both you and I know that it doesn't take much to escape from a scramble in the corner and reset back to neutral, despite the possibility of impeccable corner control and perfect play on the attacker - it's rarely seen and there's too much variables for it to ever happen; i.e not optimal distance, wanting to save Baroque, missing the link, and other factors.
About that bold part. Right, why wouldn't that be the case? You can't cancel into a Mega Crash during your active frames. So, the only feasible cases that this happens is that you just baited out a Mega Crash, to which you just made a read, you should get rewarded for that. Though, I'm sure most characters have better punishes than a Mega Crash combo.
Don't get me wrong, Tatsunoko vs Capcom was a fun game, but I'm very wary when it comes to capcom actually EXECUTING gameplay mechanics anymore. At least we live in an age of patching games, but the amount of damage something like that can do to a fighting game's reputation is not easily recovered.
You're not on that ship alone. There's a good portion of folks being wary about Capcom, in general. Especially, when it comes to anything fighting games related; myself included. Funny that you mentioned patching, though. We already have one egregious case in SFxT, where v.2013 did a decent job in ironing out a good portion of the problems the game had. Except, the fiasco with the on-disc DLC, timer scams being heavily prominent, EVO pushing it to be a four-player game, and with USFIV on the horizon, it did such a number to its reputation where the game was overlooked.
SFV seems to be heading down the same direction if Capcom thinks that changing frame data for Season 2 is enough to solve the fundamental problems with the game.