I think they were trying to set it up for a sequel. Personally, I wouldn't mind a sequel. I just went back and beat Republic Commando for the 2nd time, and I still think its a cool game.
I wish the command system was a little more free flowing. The Squad follows your commands better than any other squad-based game I've played. I just wish I could choose where I want them to snipe from, rather than the game deciding for me. Something closer to SOCOM, but with RC's AI would be perfect.
Also, I wish the Trandoshans were a little more Bossk-like. I don't know where Bossk would even fit in with the Trandoshans in RC. And I'd love to fight other enemies besides Geo's, Trandoshans and droids.