The game was rushed really badly for Christmas, so the ending was mostly not finished, Malachor V was apparently supposed to have a lot more stuff, there was a Droid Planet and so on. There is a patch called the Sith Lords Restoration Project that adds a lot of stuff back in, but yeah, the ending does really suck.
Oh, here's something even more infuriating. After the rushed release, Obsidian went to Lucasarts and asked if they could release a patch with all the missing content. Lucasarts said no.