The 3.6 is pretty well maxed out from the factory so there is not much you can do short of a supercharger to make big gains. Ensure you have a true dual exhaust (two pipes from front to back, not the funky single pipe that has a "T" split to the rear resonators). If you have the crap system (pictured) swap it out for either a Solo, Borla, or Corsa cat back depending on your budget. The rest of the systems available sound like schizz, especially the Flowmaster & Pypes systems.
You can put a better intake on it, as long as it is a CLOSED box system. I have an AFE Momentum GT on the wife's Rallye and I just installed an RPM Performance intake pipe and Hellcat lower airbox.
Before you do any of that, take a good look at which brakes you have. The regular SE/SXT have tiny 12.6" front rotors with single piston calipers and useless 3/8" thick solid rear rotors. If you do have this garbage "BR3" package, the BR5 from the RT bolts right on and you get 13.6" front rotors with dual piston calipers and thick vented rear rotors--makes a huge difference in stopping power and repeatability (the SE brakes are good for one hard stop only).