Poor decisions during launch on several fronts that, while mitigated to various degrees in the months that followed, carried a stigma that the game could never really shake.
To elaborate:
1) The game was badly balanced and glitchy on launch. Certain characters were WTF amazing, some - mostly Tekken characters - were atrocious.
2) Many of the game's systems were badly designed - boost combos, tags, cross assaults, pandora mode and gems were loved by some, strongly disliked by many.
3) The game is a visual mess.
4) The community quickly discovered that Capcom had locked 12 complete DLC characters on the disc, along with a variety of gems.
5) A whopping 5 console exclusive characters for the PS3 version, including Troll Megaman and Mokujin Pac-Man, neither of which had any excuse to be exclusive.
6) The autoblock gem caused a lot of ire when launched.
7) Throws were extremely bad - 7f on startup for very little damage. This lead to hyper-defensive play, known as Jab X Timeout.
8) The music... oh sweet lord the music. With classic crossovers like MvC and CvS being well loved for their scores, tracks like Pitstop 109 made people actively avoid some stages, unless you liked...
9) Trolling - Capcom's addition of a colour edit mode was appreciated up until the point they released the neon glow colours. An already negative community reaction overflowed into active distaste for some when all-neon characters became the new Blanka Alt 3 Meta online.
10) Evo mandated a 2v2 rule for tournaments, which was just about the stupidest idea known to man.
11) Due to the fact that you have two lifebars, games could (and still) take a long time to finish, which only forced the hyper defensive playstyle further into dominance. If you had any kind of lifelead at 20 seconds left, you almost certainly had won the round.
12) The game was a very easy target for the not-Capcom communities to blow holes in.
13) Marvel was big at the time, and the hype vs anti-hype was a big contrast.
14) Cross Assault made the FGC look like sexist children.
15) The game was utter garbage, and still is to this day.
Go watch a SFxT tournament. Any one. It's a dull, samey experience which does not encourage you to play the game.
SFxT is the best modern example of a 2D fighter commiting sudoku. Dissect it and you can find a lot of what-not-to-dos.