Basically iv got my eye on 2 different Ibanez's.
The RG3EXFM1 and the RG3EXKA1.
(im not sure on the rules of linking to websites, but they both can be found with a google search)

Both are hardtail, basswood bodies with different top woods (one flamed maple and the other koa)

In this price range will these different tops make much of a difference tone wise or are these all aesthetic?

Ill probably change pickups in the future and build up my pedal board, but tone-wise im looking for a paul gilbert or steve vai type sound.

Will there be so much a difference btwn the 2 woods that, after going through a pedalboard, I should chose one over the other to get the tone im looking for? Or are the differences purely aesthetic?
Those are veneers, not tops. Should sound very similar.
For the record 3xxx models are prestiges, Like rg3550.
On most Ibanezezesezs the top is only about a quarter of an inch thick, and that's if it's not a veneer. I doubt it'll make any significant difference, especially once when you add pedals and amp distortion into the equation.
Thanks for the quick responses!

In this case, since they would both sound similar then, Ill be going with the koa top!

Im wondering about that Wizard III neck though. I know its rounder, and I know the only true way to see if ill like is is to try it for myself, but no guitar retailer in my area has an ibanez w/ the wizard III, only wizard II's.

Is it still flat, even though its rounder? Ibanez always touts their wizard necks as "thin, flat and fast", so with the wizard III being rounder, will it then be "thin, flat(ish) and fast"?
Yes neck is quite thin, D shaped and really fast. Its a little rounder then my wizard prestige, but not by very much.