I've run many stock systems, Futaba 3PJ, JR XS3, Nomadio....stock works fine for most things and since most vehicles come with a low-end radio that's entirely functional, it's hard to pony up the dough for a nice system.
That said, the digital systems have a ton more control, some of which can be really nice, even on a basher. My favorite thing is the multiple models they can handle. Using one radio for several cars does simplify things a lot!
FM is better than AM as well. Much less glitchy and usually a better range. You can get a digital FM crystal-based system for under $100 or the same thing in AM for under $60. They're starting to get hard to find, though.
The 2.4GHz systems are awesome (very fast, no crystals or channels, feedback), but they are expensive.