SGDK2.1 does have a built-in frame rate limiter as well, which helps, I'm sure.
There are a lot of hurdles to get over getting SGDK2.1 games to run in Ubuntu, but once you're over them, it's much easier the next time. Admittedly, you still have to recompile the projects after removing a few calls to Windows APIs dealing with Joysticks that Mono doesn't support.