[Arnabas]

True enough, you can fight manually. I never really bothered. Still, the thing that bothered me most was the first officer. A typical mission went like this:
Me (thinking):What should I do. Maybe I'll scan the--
1st off: Why don't you scan the ship?
Science off: They have the kidnap victim sir!
Me: Hmm... Ok, then beam--
1st officer: Why don't you beam him off the ship?
(beam him off)
Me:Ok, let's warp--
1st off: Let's warp out of here!
Weapon's Off: Sir, the enemy is following and moving to attack!
Me: Bring us around and--
1st off: Lets turn and attack!

It drove me nuts. It must have been called Bridge Commander since you are actually just a commander, not a captain. What's-her-name is the real captain.