Not a big deal, actually. The new Tomb Raider games and the older ones, especially the classics, have very different controls, but I can easily switch back and forth between them because they're so different, look different, and require different keys, that there is no chance of mixing them up. When two games are just different enough, it doesn't matter which one you're playing, you'll manage. RE6 on the other hand uses pretty much the same third-person over-the-shoulder shooting mechanic as Rise of the Tomb Raider, which is why I keep getting confused and trying to make Ada do stuff that only Lara can do. Switching back from RE6 to RE5 is an even bigger challenge, though.
It's like trying to speak two foreign languages that are just too similar (like Spanish and Italian), causing you to use words from one language in a sentence of the other language, whereas you don't have that problem with a third language (like French) that has similar grammar, but completely different pronunciation.