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If that is all you have to fix, you should definitely stick with him. Tell him nicely what you'd like him to change about his appearance, but also make sure you tell what you like about him and that you appreciate him.
Do you really like him? As a person I mean, or do you just like how he treats you? And just curious, what attracted you to him to begin with if it wasn't looks? Where you friends? Really liking them is accepting them totally. Having said that, I also believe you shouldn't "settle", they can be great "on paper", but if you're not physically attracted to them, that's important also. So maybe he's not the guy for you then? You might just be afraid you won't find another guy that has those same qualities, but you will. He's not the only one.