AOTL is unfinished as far as I can tell. On the website where you download the zip file, there is a seperate DOC file you can download that explains how to pick your character (it's a clunky system, but they claim it was the best they could do).
In the beginning when the idea of using command lines was introduced, I found it tricky at first, but then I realized that many other games used this type of patch running, so I became familiar with it. Then when Patch Commander was released, I had no trouble, as the program was so easy and user-friendly.
Once you learn how to use patches, it becomes second nature. Granted some patches are just super buggy and don't work, but that's the fault of the author(s), not of Jedi Knight or of Patch Commander.