SPECIAL is fine, if you ask me. Why change it? Anything else you come up with will just be another arbitrary stat system, and Fallout, with the exception of Tactics, has worked well with this one so far.
I would much sooner change the skills. I liked where VB was headed.
You bring up a good point though...how exactly should it tie in the skills? Should stats have a bigger impact on skills? I think so. I think a physical character, with high strength and agility, should not just be a little better at melee and unarmed. They should be a lot better. If you are an above average physical specimen, you should start with above average physical skills.*
Anyway, bottom line, I think stats should have a powerful impact on skills. F3 tied every stat to skills, which was good, but I don't think they went far enough. The starting character is not really good at anything, which kind of sucks. There is no reason you can't be good at something right off the bat. It would add some more weight to character creation.
*What is an average level of skill in something? It should be addressed.