To the OP, if you have an SGX then this should be a no brainer. If cost is an issue, then Turbo ED.
I'm not a big fan of Capcom's FM usage in their arcade games (too thin and steel-y). The Genesis version FM sounds much better than the arcade. But I like the charm of the PCE's audio chip in this game (as well as 1941) over the arcade original tunes. I never had an issue with the controls. Overall, the graphics do definitely have a better appeal to them over the Genesis version, but it's not like comparing the two Forgotten World ports.
If you're looking for a PCE experience, get the SGX one. If you're just interested in the best port, then look else where.