Look closely at the Settings section of the launcher, with your eyes, inch-by-inch. You'll find it.
it's grayed-out unless you have Steam Integration off, and it lets you choose between:
- Original Jedi Academy engine. (JAMP)
- An engine based on OpenJK, an open-source update made after the Jedi Academy source was released. (MB2 Client)
The MB2 Client has its own unfortunate quirks. Minimap arrows are all the same color instead of distinguishing between allies and enemies, and the HUD is stretched in widescreen. I don't think there's any real reason to use MB2 Client except if it happens to just run better on your computer. It might.