What makes using OBD2 system, so much better than OBD1

OBD means On Board Diagnostics. OBD II has far more system diagnostics than OBD I. Most OBD II systems can be flashed via a programmer (if supported by the aftermarket) where as OBD I needs a chip, reprogrammed, or replaced with a different ECU if major modifications are made like a larger cam, larger injectors, added engine displacement, etc. On the trans side I don't know, some manufactures the ECU controls the trans (if electric) and some have a Transmission Controller (TCU). If you have a donor, use all the stuff from it. Mismatch is when you get into trouble.

This is why the LS cookie cutter stuff is so adored, the aftermarket made it like playing with Playmobile instead of a used Lego set with no instructions. But, I'm a Lego guy.