I think the number of broken combos and infinites in MBAA's original release version really strained their trust in the game
what is unlimited codes doing there then
Unlimited Codes has annoyingly broken-ass combos, but no character has an easily accomplished infinite(and as far as I've seen I believe the infinites that were in the game have long since been removed by rebalancing. Saber's, for example). Certainly the combos are rather over the top, but no moreso than guilty gear(hello Slayer).
HnK getting two years at SBO honestly did confuse me when it happened, but still, that game requires some execution difficulty. There's a difference between an infinite that requires strict execution(See Denpa's Satsuki infinite in MBAC B2) as an infinite that is just mashing one button repeatedly more or less(Ciel Key infinite in MBAA). You can look at HnK and, even though the game is broken, at least look at a player and see that he didn't win purely by spamming one broken move, he had to learn how to play the game. That's true as well of F/UC, which is also an execution-heavy long-ass combo centric game much like HnK(although in my opinion it is arguably far more balanced than HnK ever was). It's even true of MvC2 despite how much I dislike that game. People do not win major tournaments just by mashing buttons.
MBAA in it's original incarnation was far far too broken to be considered playable in a competetive scene. Now it isn't, but that probably stressed Tougeki's trust in the game, and I imagine they're taking a "wait and see" approach currently.
As for MBAC Ver. A's Sion infinite, well, yeah, that was dumb as all hell. Perhaps that whole fiasco is the reason they're being so reluctant to have a second recurrence of that?
As for TvC, well, I don't like the game, but I am not fond of any of the vs Capcom series other than CvS2, that's a personal dislike.