Hypertech will make a big difference. How much? I'm not sure, they don't make them for 11-12s, only the 08-10s.
As for everything else, some claim yes, some claim no. Personally my friend on 32s and 4" lift used to barely pull on me when I was stock. All he had was a Brute Force Intake, super 44 muffler, and maybe a Jetchip(but I don't think so). There could be a ton of reasons behind this though. He could have hit the gas sooner, the programming differences between 08-10s and 11-12s, slight differences in manufacture specs(mine could have slightly less power, his slightly more), etc. Like I said, he barely pulled.
All that said, it's not worth the money to me for no real performance gains. Especially since the ECU will change everything to perform like stock eventually. If you wanted to change the sound then sure why not get an intake.
2011 Deep Cherry Red KK - Skyslider - OME 927/731 - Bilstein Shocks - 1/4" Spacer Plate - 3/8" Clevis - Al's A-arms - 245/75-16 Duratracs