For some N64 games, the GC controllers work really well. But for regular most other VC games (Genesis, NEO-GEO, and SNES especially) the Classic controller is the best. It's actually not uncomfortable, and is generally easy to use.
I say to go with that for the sheer fact that no VC games are optomized for use with GC controllers. They are optomized for use with the Wiimote and/or Classic Controller, however. GC controllers come with bizarre "automap" functions which place the actions in the most uncomfortable, or unreliable of places. It comes with the face buttons being a completely different set-up from the SNES/Genesis/Neo-Geo/etc, and the fact that the D-pad just sucks overall.
I'd say to get the Classic Controller. It's comfortable, it's functional, and most importantly--it's the controller they go by (along with the Wiimote) when releasing VC games.







