I think the biggest advantage is tunability. A very close second, is fewer things to go wrong.
The aftermarket setup doesn't need to see engine RPM, barometric pressure, brake light status, or PSOM (part of the cluster). There are probably other sensor inputs that I'm forgetting. I think the PSOM integrated cluster was only for 1992 and newer trucks.
The older system I have isn't perfect. It doesn't properly anticipate when to unlock the converter in anticipation of an upshift. This is not an issue if you only allow the converter to lock up in 4th, but I have mine programmed to engage as low as 2nd gear. It's a minor driveability concern, but still annoying enough that I may upgrade to the newer controller eventually. I was told by someone at US Shift that they have upgraded to a more advanced converter control logic that can keep the converter locked during a shift, or even attempt a limited slip during a shift to control shock loading on the driveline. It sounded very interesting.
For reliability, it's been way better than any aftermarket setup deserves to be. The only feature I was never able to figure out, was the "manutronic" function, which uses the cruise control buttons to upshift and downshift. The only failure I ever had was a broken wire inside the connector. The controller itself has functioned flawlessly for over a decade now. Karl Baumann knew how to build a good product. If he was involved with designing the newer evolution, I would feel confident that it will be just as good.