Two bug types, of relatively common types, that happen to be both quite good anyway.
The thing that they have in common is that they are both pokémon inspired from two ancient giant arthropods.
Who would win in a fight?
Which is more useful?
Which has a better design and concept?
Which do you preffer anyway?
Anyway, I think Yanmega would easilly defeat Scolipede, having many options to do more damage, coupled with stats and ability.
Similarly, while it is weak to Rock, it can be quite destructive anyway and hard to get rid of. However, Scolipede (ironically) plays a little less agressively, and it is good for starting battles.
As for desing... a giant centipede that looks like the king of all that crawls is a pretty cool design, but Yanmega gives Bug types a pretty terrific and intimidating image.
If only it were Bug/Dragon...
So overall, I'm going with the flying one.