Well, thats a hard question
Because even a jvs, and even a fast io have limitations, as to what controller is plugged into them Meaning you could have a fast io, but with out the gc controller its not going to be very playable with said joystick setup
so I am going to assume you mean what stick and button games are playable on both
For JVS, You have the option to run nikos multi and boot all original None fast io games, Everything form Kof 98 To Kof Climax, to street fighter 4 arcade edition
You cannot run most nesica titles, however there is a few you can and those are battle Fanstisa, 3d cosplay mahjong, Samurai spirits sen , BBCS2 and kof climaxx nxl version both accept fio and jvs.
With JVS you are also able to run Nikos, JVS to keyboard code, thus turning your jvs device into a keyboard as seen by windows xp, this enables things like mame and other home-brew apps to control.
For Fast io, You can run every game designed to run on a fast io, so games such as ultra, nxl titles, ect including nikos multi however your not able to then go and play JVS titles, however
Corey has released a fast io to keyboard much like the one above, that enables you to homebrew up just about any software you would like
as to what id say is best, well personally a real rfid and fast io, because you can then play just bout everything, today was a jvs, is limited.