It should work with a Voodoo 5 5500 AGP, but may take bit of tinkering.
When I first installed and ran the a similar game such as Medal of Honour: Allied Assault, none of the video sequences at the start would show and the menu system's text was so horribly corrupted that it made menu navigation impossible.
Heres how I fixed it:
1) I downloaded WickedGL from http://www.wicked3d.com/technology/wickedgl.htm
and installed it.
2) I went into the dir where I installed Medal of Honour: Allied Assault and found the exe file, and I renamed it quake3.exe
3) Then I ran the WickedGL control panel, and told it to look for the game Quake 3 in my Medal of Honour: Allied Assault dir.
4) It told me it had found a copy and asked me if I wanted to install the MiniGL driver there, so I clicked OK.
5) I closed the WickedGL control panel, went back into my Medal of Honour: Allied Assault dir and renamed quake3.exe back to its original name
Now when I run the game I get the WickedGL shareware message which says press 'C' to continue, and then the game works fine!
My PC is as follows:
Voodoo 5 5500 AGP
SB LiVE! Value
Windows 2000 Pro
The game runs like a dream on my machine in 800x600x32
This should also work with Jedi Knight II seeing as though the graphics engine is also based on the Quake 3 engine. Give it a try and make sure you have the latest drivers for your card!!