I think Destoroyah would win this. Destoroyah managed beat the everlasting crap out of Godzilla (in his burning form no less) and junior by himself, whereas Mothra and Battra were forced to team up to get the job done (just barley).
Mothra and Battra may have the speed advantage, but they're SERIOUSLY lacking in the durability department. A swift bite from Godzilla was enough to kill Battra. Just imagine if Battra (or even Mothra) got hit by Destoroyah's horn slash! It would spell disaster for the insects (especially if he managed to cut off their wings). Destoroyah's micro-oxygen spray would do a number on the pair as well (the ability was derived from the flippin' oxygen destroyer after all!). Mothra's and Battra's beam attacks would do minimal damage at best. I mean come on, Destoroyah was able to withstand several atomic blasts from Burining Godzilla. I think he can handle a couple of light beams. Furthermore, Destroyah has the ability to fly. Battra and Mothra have absolutely nowhere to run.
Don't get me wrong, I'm not trying to put Battra and Mothra down, but they don't stand a chance.