I must comment and also say that this is ides is, personally, great.
I'll try to detail how the idea I read here went throught my head:
"...ooh. Cool. Banana. Hmmm. Hungry. Donut. Ohh. Commaders in GalCiv 2. Cool. Banana. Hmm..."
And now for being serious.
I think that every ship you'll build will be assigned a commander automatically, without you inteferring in the process. The commander will be given a name, planet-origin, a random picture, and that's it. If he'll survive long enough and succeed a couple of battles, he'll go up an experience-rank, which will give him a bonus of some sort, like the bonuses that were mentioned earlier in this thread. Maybe even a battle resume could be added to each commander - showing that he participated in the "War of the Eastern Galactic River" and such. And another insignia would be added to his military outfit in his picture.
Eventually, I think that each civilization will have one, two or three respectible commanders which succeeded a lot of battles. When this top-notch general will advance towards a battle, the AI will think twice if they can battle him with success. So, I think it'll add to the element of fun to try to kill your rival civilization's top commanders, and they'll try to kill, or overcome, yours. Huge battles with the best commanders your civlization has to offer wil join together to battle a rival civilization, which will also gather up her best commanders. This could result in a real epic battle, where many great men will fall, but the commanders which will survive will be considered heroes that have outwitted their opponents.
Perhaps if a commander get promoted enough, and by enough I mean A LOT, the civilization he belongs too will recieve some kind of bonus. Like a small moral boost due to pride that 'this great man is one of us'. Having the most fearful, experienced and cunning General could help your civ. However, only the civ with the most experienced commander will have that bonus, so unlike a galactic wonder, this 'title' could change from civ to civ throughout the game timeline.