Saw this and wanted to add my 2cents.
I'm running a slew of different branded parts of my car including APR, Uni, GFB, 034, and AWE (this is just my engine we are talking about here). I started with an APR intake and didn't like how the recirculation hose didn't sit squarely into the stage 2 portion. Switched to Unitronic and it fit very well after I had to the cut the intake hose piping that wasn't quite the right length.
I had an APR turbo back exhaust and overtime noticed leaks at every single slip-fit joint and then tried Unitronic who used V-clamps. Now no leaks and flawless fitment.
Throughout this process I have always stuck with APR tuning. I'm currently using their k04 and it's flawless. Really compliments the car well on and off the track.
You mentioned all the different tunes that you'd be able to utilize with the Cobb AP, however, how many tunes are you gonna need? I have my 91, 93, 100, and stock/valet/etc. I use my 91 here in California, and maybe 100 at the track, other than that I never switch tunes. None of this high boost versus low boot business, just one tune that optimized for an intake, high-flow cat and intake. Just because you have access to more tunes doesn't give you greater value if you're not going to use them.
For the price of a Protune you might as well get a custom tune anywhere including 034 or any other reputable tuner. You're probably going to pay the same and you'll be limited to the tunes the build out for you. So if you're tuned on 91 but you want to run 100, well you're just going to be wasting your money since we all know the tune extracts the power from the octane.
With APR you've already got your tunes, you bolt on the minimal hardware requirements they have (intake, DP, IC), you have torque by gear management and refinement through the rev band, you're dialed in at this point and just have bury your foot and hold on.