I love mess... I've even written a utility specifically to aid the use of mess as an emulator for a mame cab.
With that being said, I almost always use it as a last resort. I don't like the hierarchy setup within mess in that a whole game system is treated as a parent and the games clones. It makes for confusion when setting up configuration and ctrlr files. Also it handles some of the games with odd chips horribly, which is due to their goal of accurate emulation. Also it should be noted that the snes is virtually unemulated in mess, so it's a moot point.
I think snes emulation has always been great with the third party emulators, but the fact that all console emu developers tend to force their own gui on everyone was holding them back. The fact that the zsnes team is back and is making steps towards fixing command line related bugs is a step in the right direction.
(the real team at that... i don't know about you guys, but the unofficial releases didn't seem to be any different than the last official one 2 and a half years ago.)