A couple more, off the top of me pointy head ... ( with regard to custom tuning):
Reduction of trans temps by minimizing slippage
Tow tunes offer reduction in EGT's at rated loads for safety
Excellent A/F control in Open Loop ( may require datalogging )
Ability to provide a specific MAF transfer function for almost any aftermarket CAI/WAI/Washoobi, to render them safe to use
Integration with Widebands, EGT gauges, and any other analog inputs for either display and/or datalogging capture ( specific to hardware device )
Actual achievement of the 300+ crank HP you paid for, as the shift points are raised to the point where this ( peak) power is available.
Improvement in power "under the curve" across the entire rpm spectrum.
Optimizations of a host of other delays or shortcomings in the factory calibration, leading to improved overall drive-ability.
Reduction of Open Loop delay.
Datalogging ( SCT has a very feature-rich set of tools for this )
Specific tuning for *any* octane level, and *any* user-specified usage ( e.g: race, drag, econo, MAX tow, perf, combo perf/tow, etc, etc
Full 7-digit Strategy-matched custom calibrations - far more in-depth tuning than any canned device can provide.
According to TP, on 93 octane fuel a good custom perf calibration can net you up to 40 hp and 70ft-bs of torque on a 5.4L 3V