I've actually had the opportunity to compare the tune files from GDE, MRTuning, SFT, Reckless Motorsports and PPEI. I recently reviewed Mrtuning's 60hp tune. Mrtuning's file is very similar to SFTs, which I'm sure will come to a surprise to many. MRtuning has only very basic modifications made to fuel, timing, and slightly increased injector duty cycles in the upper end of the RPM range. Boost is actually lower than GDEs and SFT's. The biggest surprise to me was the pilot and post injection maps are unchanged, the same sooty amount of injections/timing as stock which is also what SFT uses. The tune is however smooth, and performs well.
I can't speak for their lesser HP tunes, however.
GDE doesn't have quite as much power, but they have re-engineered the pilot and post injections and optimized them to reduce wasted fuel and provide the cleanest burn and better fuel economy. You will get better fuel economy and produce less soot than MRTuning if you go with GDE. I haven't looked at the newer GDE tune. However, based on their previous tune I'm assuming much of what they had before has moved into the EPA compliant tune. The main thing they needed to do was re-introduce the EGR. They advertise having much less soot than stock, so I imagine the pilot and post injections have been optimized like previous tunes.
If you're looking for the most power, Reckless Motorsports new tune is a step above the others are as far as power and response goes. I have yet to do full comparisons, but will be starting on those this week. We'll see how it performs to the others. I know the pilot and post injections are modified and not stock, so I'm assuming it to get better fuel economy than SFT and MRtuning, not sure about GDE though. But we will see as the increased power may make up for any fuel economy gains. I am dedicating about 10 hours a week to these comparisons for the next few months.