I run FS9 on two computers with Vista - Vista Enterprise and Vista Ultimate.
Both computers have UAC active and I have no problems with FS2004, or FSX.
However, I did not install FS in \Program Files on either computer. I created a folder C:\MS_Games and installed FSX there. One computer has two hard drives, on that computer I installed FS2004 in D:\MS_Games.
My experience is that FS2004 works better when not installed on the same physical drive as the OS, while FSX is best installed on the same partition as the OS.
Your mileage may vary.
The biggest pain for me with FS2004 on Vista is having to disable my advanced desktop theme. I find that FS2004 works best when I set the theme to "Windows Classic" before launching FlightSim.
@ PawPaw's house - near KADS, Addison, Texas, USA