Well what do you want out of the car? Are you looking for performance mods, to just change the sound, do you want it to handle better?
If your looking at the exhaust and you want to go to a true dual exhaust, there are lots of kits. Make sure the new exhaust has cats, mufflers and ports for the correct sensors. If all that is there it shouldn’t affect the way the computer runs the motor much. The farther from stock you go the more the computer tries to compensate. For instance if you went to a dual exhaust with no cats, mufflers or sensors, you would need the dummy plugs for the sensor wires. Those would tell the computer that everything is normal and not to throw codes. Then you would want to have the ecu tuned to compensate for the dramatic airflow changes. Before you do any tuning make sure you’ve performed any other performance mods you plan to do, like CAI, cams, turbo etc. that should all be accounted for before tuning is done.
For other more serious performance mods, the biggest bang for your buck will be a turbo or centrifugal supercharger kit. Cold air intakes (CAI) are a few hundred dollars for a few horse power and come with questionable air filters. When it comes to performance air filters just remember that the more freely it breaths the more crud it lets through. You could also order custom cams to change valve timing and prioritize more power over mpg. But that will get pricey. Not that a turbo kit isn’t. You could also get away from the tall rear diff gearing and go with 3.70 rear end gears. Will dramatically change your acceleration and driving experience. Changing the rear end gearing will require you to have your speedo recalibrated. If all you want is a more aggressive sound then buy a different muffler. That won’t mess with any thing else by it self