I was thinking about this, too. Then I started to have more and more people tell me, and point me to articles about engine design and tuning, and the more I learned, the more I realized that Suzuki/Geo actually intentionally designed the air intake to cross over the hot exhaust for a reason. It acts as an "intake air heater." All this talk about "cold air intakes" and such, and there actually is such a thing as having air that is TOO cool. It crosses over the exhaust for a reason.
I left mine alone. The only thing I am trying to change right now is the fact that the factory intake tube in the fender has two inlets: one next to the headlight drawing in fresh outside air, and another inlet in the engine compartment behind the headlight about 1" around. I would suggest (and I am trying to do this now) ducting that 1" inlet to just behind the grille with some kind of air "scoop" to be drawing in cleaner/cooler air, not from inside the engine compartment. Then you retain the original "intake air heater" that Suzuki engineered for a reason. Believe me, there's plenty of things that we look at and think "why the hell did they do that?" when actually they did lots of R&D and engineering to come up with things.
I'm fooling around with this right now but haven't come up with a real good idea.
I was going to use an extra-wide Shop-Vac tip and some 1" flex ducting. That's my "prototype" idea. If anyone has any better suggestions, throw them out there.