Thanks to Lo's membership+friend card, we've been to both of these in recent weeks. I have to say I think I preferred Bacon more, maybe because it was a complete retrospective rather than a late period and so contained more variety.
But I think also the Bacon one is slightly better laid out, with a real sense of progress as you go through it. Rothko has some strange lighting but maybe that's more about what he was trying to achieve with his paintings. You could stand at one end of the big room and get a much better idea of what he'd painted than when you were close up and it mostly just reflected the lights. Still, it's clear that no matter how simplistic his designs look, they're really quite complex when you see them close up and examine how they're put together.
The Bacon hasn't got much longer to run so I guess you should go and see that soon if you're interested. The Crucifixtion room is particularly great, if a trifle disturbing.