The engine's a 1.8L 7AFE, ~105HP, ~115lb/ft of torque.
If you're looking for considerably better highway merging/acceleration, consider intake/headers/exhaust. The F means the head is designed for fuel ecnonomy, which means you're not going to be able to see terribly great gains out of that engine unless you either make a 7AGE, which means putting a G-series performance head from a 4AGE engine on the 7A block (the 7AFE is basically a 4AGE with a stroker crank and narrow-angle slave-cammed head, I'm doing a 7AGE conversion in this thread:
http://www.toyotanation.com/forum/t98590.html ) or turbo the F head or do something silly like NOS. NOS is, as always, the temporary solution. Because of the design of the F-series head, it'll hold up better to turbocharging, but everything is going to be pretty much custom piping if you go that route. That means big $$$ in most cases. Of course, you could always drop a 4AGE 20v or 4AGZE (supercharged) into the car, but, again, that's going to be pricey, and it's kind of cheating the question of how to work with the engine that's already in there.
Your best bet is to do the simple airflow stuff for s'more highway grunt, and work with the strengths of the car, to wit, decent handling and gas mileage. Stiffer springs, aftermarket shocks, maybe slightly bigger rims and slightly lower profile tires. Throw in a front strut tower brace to fix the oversteer, and you've got yourself something that'll hold its own against traffic.
Obligatory brand suggestions:
OBX and DC Sports make good headers.
Ractive makes a capable short-ram intake that can, with a little work, be positioned such that it won't function quite so much as a hot air intake.
Best bet for exhaust is either get some mandel-bent pipes or go full custom. Leave the resonator in, though.
This is all just based on personal experience, mind.