MESS is fine for some systems. Specialized emulators will have greater compatibility and will be faster and more faithful to the original console or computer. Some systems that MESS try to cover simply don't work at all at this moment (Odyssey 2 and PCE, for instance)
As a rule of thumb, I use MESS (with MALA as a frontend) for everything. *IF* I'm not satisfied with the compatibility on a certain console, then I go and find myself a specialized emulator for that.
The great thing about using MESS is that you have a common interface (tab menu, etc...) to all your emulators and it is very similar to MAME.
On a side note, MAME Plus is incorporating some of the MESS drivers, which I think is a great idea. I hope they go on with it and incorporate all the working/stable MESS drivers.