I think Seth Killian mentioned in an interview that you can opt-out of choosing gems, but you can't turn the system off entirely. Either way, if the game was designed with the gems in mind and you need to turn them off to make it competitive, it's probably not worth it.
Smash Bros comes up a lot in the discussion due to the community-wide ban on items and most of the stages, but really, that game is so unique that turning off everything that makes it awful in order to keep it on the table is a viable option. I doubt SFxT will be worth the fuss.
Even if the gem system stays in and works out, you know as soon as someone finds the right combination of gems on the right characters in the right team, you're not gonna see anything else. There is a enormous number of possible gem/character/team combinations (talking billions here) that it's impossible for the developers to balance, and in spite of that astronomical number, someone will always discover the broken shit in no time at all. It's J.Wong's Law.