Part IV: Upgrades
As I mentioned earlier, the car already had some upgrades courtesy of Yokohama, Enkei and TRD. The exhaust had a healthy note to it without sounding too rice at all. It was a deep, mellow tone that sounded very good. Not as nice as a nice twin turbo BMW inline-6, but still nothing to be ashamed of either.
The tires were what they were. I've had Yoko S-Drives on my Mini Cooper S and MR2 and like them since they're a very grippy tire that's also progressive at the limit and communicates exactly what it's doing. After driving with them, I'll probably put a set on my FR-S after I burn up the stock set in the first 5k miles.

Now for the good parts. As seen in the picture below, there is certainly room for an intercooler above the engine with a hood scoop to provide fresh cool air over it.
This picture is taken above the front of the engine looking down. There is room between the front of the alternator/serpentine belt and the electric fans for a compact supercharger in my opinion. The small tube running off of the intake in front of the alternator is the resonator tube that routes the sound to the inside of the cabin. I'll remove this before my first day of ownership is up most likely. Hey, less weight, right?
Supercharger not your thing? How about a turbo? This picture is looking down in the rear passenger side of the engine bay. Between the battery and main engine, there is a large area looking straight down on a section of exhaust between the end of the header and the catalytic converter. Looks almost like it was left empty for a possible future turbo!
The intake looks like it could be opened up, since I have no idea how that 90 degree bend and the sonic tube could possibly provide smooth airflow to the engine. I'd say you could likely gain a little power with a more free-flowing intake, but that is merely speculation.
Aerodynamics: I don't think much will be needed here unless you're running very high speeds. The underside is very smooth and you can see how sleek the body is. This picture is looking under the front of the car towards the rear.
This one is from the rear looking forward:
Questions? Thoughts? Ask away and I'll answer what I can based on the limited time I had with the vehicles...