Jaguar eschews a modern day GUI in favour of a simple approach: games, and games only. And it does an excellent job with games, too; every Jaguar game comes in a bundle, along with a full manual which is pages long and handwritten on a per-game basis. By having nothing but what it needs to, it also allows a more refreshingly retro gaming experience.
Jaguar is a totally open platform. You need no licensing or permissions to develop for Jaguar - make something, tell Game Fusion you've made something, and it's ready for retail - no questions asked.
Jaguar also allows for developers to use their very own APIs with more convenience. With Jaguar, developers are allowed to copy their APIs to /apis/ for easy access. This not only removes reliance on loading APIs from the disk all the time, but it allows other games to use preinstalled APIs to save disk space.
Thanks to Gonow32 for preserving the previously lost source code.