El Salvador is scenic and friendly, and there's no real reason to avoid it--particularly if you don't like potholes, as it appears. I recommend the side trip up to Perquin and a quick tour of the massacre site, museum, villages, etc. San Salvador is so easily bypassed that I hardly even noticed it on the road.
No way to avoid the Honduras import fees either. Just don't over-pay, and don't be thinking you need a helper when entering or leaving. Oh, and follow the traffic laws carefully on that stretch, since no matter where you are there's likely to be a police barricade within spitting distance.
Hope that's helpful.