How badly do you hate them the way they are?
As I see it you have 3 choices:
1. Leave them the way they are.
2. Replace the crankset with something nicer.
3. Refinish the ones that you have.
I've done all three at various times. Usually, even if I hate them, I leave them alone until I get bored. Then I'll try refinishing them. The replacement option is always open if the refinishing doesn't come out satisfactory.
Aluminum isn't the easiest thing to get good painting results. Somebody once advised me to etch aluminum prior to painting by wipeing it with vinegar. I did that before I primed and painted the crankset on my beater bike and, so far, the paint hasn't chipped, flaked or rubbed off.