The problems with gems aren't so much the gems themselves, it's that they were executed horribly.
With the way they're set up now, tourneys would run to a halt if they allowed gems as you can't select them on character select so there'd be as many problems as MK had with its button config. On top of that, Preorder/DLC Gems are just stupid. Plus, when TO's do ban gems, which they will unless Capcom makes them more friendly for tourney events, the online doesn't even have a filter for non-Gem users so you can't even use Online to level up reliably.
It's just a big mess right now.