Doesn't RetroArch force everything to 60hz? That right there kind of makes it useless, because almost no hardware actually ran at 60hz. You're starting off inaccurate. The SNES, for example, runs at like 60.0984hz. The RetroArch developers don't really care about running games properly.
Personally, I'd rather stick with GroovyUME and just wait it out. It's true that MESS's SNES emulation isn't as good as BSNES's, and it's true that its Genesis emulation isn't the best (although it does run a lot of games just as well as any emulator), but it's improving basically every week. It won't be long before MESS emulates all these systems just as well as any of the standalones. Also, the sacrifices you have to make to basic emulator quality to use a standalone emulator just aren't worth it. Any standalone emulator you use is going to have more input lag than GroovyMAME with framedelay, and there's a high likelihood that it'll run like crap on a CRT (if it works at all).
Standalone emulators don't have any real staying power, because they tend to be developed by only one person, and they eventually get abandoned/outdated, and MAME/MESS will just keep plugging along.
In 2014, who uses Callus instead of MAME? I remember in 1999 when people on IRC told me that MAME was garbage for playing Neo Geo games and that we'd always be using NeoRageX. See what I mean?