[masterofweirdness]

This is gonna sound annoying, but what do you want him to do?

Commanders work best as support chars in a shooty marine army. You give him a stormbolter and powersword plus termie honors and he rocks.

Or, get a big command squad, inflitrate him with 2 lighting claws, termie honors, frag grenades, ect and he's KILLS in the assault.

Finally, you can go for the cheapie commander, powersword and bolt pistol. Not the best, but still, he's great for sweeping away hordes of MEQs in one round of combat, though against low saves its a bit of a waste...

Also, remember, each hq in the marine army, though versitale, do have differant roles and seem to do best at differant jobs. Chaplains are assault, Libririans are expensive support, and commanders are cheap support.