With the stock computer and various types of chips(TT and FT) /power logger you can have the following:
1. Lean Cruise mode - a/f is automatically set to about 16.0 A/f during part throttle driving above 45 mph and higher
Most aftermarket ecu's have a Target A/F Ratio Table that will allow you to run in closed loop at whatever A/F Ratio you want. IMO: Basing it off of MPH, isn't nearly as critical as basing it off of load. I will say that the WBO2 sensors used, don't read above 15.94 so they can't quite run 16.0 without going open loop
2. Highway spark advance mode advancing timing to improve MPG, as more load is added it will go back to 14.7 on moderate throttle.
Aftermarket does the same, based off of load
3. WOT Timing and A/F can be altered based on mph, ie different for (1st/2nd )and (3/rd 4th), but this is based on mph programmed into the chip, not actual inputs from the trans switches on TT and FT chips anyway..
Once again, IMO: Basing it off of MPH, isn't nearly as critical as basing it off of load. If you want to base it off of mph, the XFI has a work-around for it using the Aux MPH output
4.Different pre programmed idle speeds between park and drive along with different IAC operating curves based on p/N switch input.
The aftermarket does not have this, but it could be done by wiring the p/n switch into the system. I have never seen an advantage running two different idle speeds
5.A/c request IAC motor bumps idle .4 tenths of a second before engaging compressor to help stabilize idle.
XFI has this
6. Fuel Decel enleanment based on speeds over 12 mph to reduce richness on decel and full fuel shut off DFCO, (depends on chip)
XFI has decel enleanment based on TPS position and engine RPM
7. BLM's which allows constant small fuel corrections to avoid big swings in a/f ratio at lower speeds. Basically a self adjusting VE number to maintain 14.7 a/f once in closed loop.
The aftermarket is generally run in closed loop all the time. Once the tune is close this adjustment is a non-issue
8. Stock o2 sensor is used for tighter a/f control for cruise, but wide band is automatically used in boost based on maf grams.
Aftermarket does the same thing, based on MAP instead of MAF
9. Increased Data logging with a power logger 55 items can be logged at about 18 frames per second at once.
XFI can log 48@20 frames/sec WITHOUT a laptop in the car, BS3 can log even more using the Replay feature
There are draw backs which I'm sure we can discuss too.