Apologies if I'm late to the party -
I know it's not one of the systems specified, but ST: Tactical Assault for the PSP is a prettyu good game. It's like a toned down and simplified version of ST: Starfleet Command, or ST: Encounters. I believe they also make a version for the DS.
Yes, there's a version of the DS, and while it's simplistic it is still a whole lot of fun if you can buy it cheap. The PSP version may have better graphics, but the DS one has actual working LCARS buttons on the touchscreen, which has got to count for something. Running you finger over the screen to set a course or jabbing at the "go faster NOW" overdrive button is almost worth the price of admission alone.