The thing with the MX-5 is that it's got a chassis that just makes you want to thrash the living daylights out of it and at the sort of power levels they have as standard (160 odd BHP from the 2.0 NC we have) you can do that all day long without it ever getting seriously out of shape or losing your licence. There'll always be long straight bits of road where you wish for a bit more grunt, but on the twisty bits where it counts it's more satisfying to have to stir the stick a bit to keep it going rather than have a big V6 where you just leave it in 4th and use the torque.
I think if I were going to upgrade one, I'd go forced induction. In fact, the ecoboost I've got in the Jag started off as the Mazda L series anyway, so I wouldn't mind betting it would drop straight in and give you 240 BHP. Why you'd mess about with a V6 I don't know.