Besides the obvious body style change from '99 to '00, mechanically, what all did they change? I know they didn't touch the engine, did they beef up the trannie, suspension, etc.?

I just worked on an 2000 SE and it had a weird Air Pump

Don't think the older ones had the air bags in the back

Things are tighter under the hood. I believe they changed the passenger side engine mount from the side of the engine to the bottom. 4 wheel disk brakes on the 00+ I believe they still had drums on the back up till 99

Correct. My 97 had drums in the back

From a drivetrain perspective little changed.
96 Sc had the 4T60 trans
NA had the 4T60 trans til 98
The 97 4t65 has some minor differences vs 98-02
The 03 4T65 had the upgrades to valve body and 4th hub shaft

Engine wise some 2000'* had the california air pump emission stuff.
96-97 had an evap purge switch and purge valve, newer only had an evap valve.
Minor vacuum differences, nothing that made a difference though

Overall just some refinement.