I'm firmly on the side of multiple FarCry2 style characters being pointless and confusing, unless there is an effect to the story, and unless the extent of that effect is made clear at or before the point of selection. Besides, one character no options fits the game intentions best, as I currently understand them.
You have a tight story, so I'm thinking Max Pain, which is heavily story and personality driven. The personality is almost more important, as with Duke Nukem, which was wildly popular. Another angle is, Trek's captains are very individual, you can't just switch in a random captain for the same results. There may even be an expectation to have only the captain you get, since that's how Trek series work. By following that example, you have the chance to create a popular character, rather than only a popular game or story.
Another angle to consider this from is how Commander Sheppard is very popular in his default form, despite there being character customization in Mass Effect.
The only arguments against I can really think of are, STO has character customization, and the story will have player decisions being important. The latter one potentially fits in with the BioWare games, which all have various levels of customization, and which the Mass Effect example goes against. The former isn't important for several reasons I won't get into.
If it's determined customization is critical, then what about using the one character model, but with different hair styles. That way, hair morphing in-engine isn't needed, and it takes less work than full characters because you don't need to come up with different backgrounds which segue into the story, nor morph facial models, nor body models. It also allows mid-game appearance changes, both controlled by the engine and player.
Imagine being taken prisoner for weeks, or months, the man's beard is going to grow. Or, maybe people who captured him are expediant and just cover his entire body with nair. You'll have a bald captain, no eyebrows either.
