For the rank: I don't think that anywhere colonels' lead only one squad unit on the field, but maybe they could have hinted that you would be leading some other special forces squads too. Colonel would be leading the whole battle in safe distance. So it makes sense that you don't get promoted. Major is little iffy by itself already in my opinion.
But yep. The ending was a let down if you have played Jedi knight first.
I think they watched way too much SG-1 when they made the ranks. Colonel
Jack O'Neill anyone?
Seriously, the promotions in this storyline happen A) way too fast, and B) he's commanding far too few people to warrant a promotion.