Sometimes Webber is in a different car, but you are also assuming that new parts always work out better, they don't and its only sometimes they don't put new better parts on both cars. Yes they often put a new wing on one car or the other in practice, and see if they can see a noticeable difference with them, but they then often put the new wing on the other car before a later practice session, because ultimately the same driver using both parts tends to be better.
I'm fairly sure I remember Vettel trying a new wing, not liking it and going back to the other one. Ultimately you need the difference to determine if new parts are indeed better.
In general Hamilton and ALonso are deemed better drivers than Webber, and Vettel is deemed better than Webber, hence it would be MAYBE a better competition, ultimately it doesn't work out that way.
At Mclaren Hamilton might spank Alonso, but put both drivers in Ferrari and Alonso might spank Hamilton, at RBR they might both be identical, it could be Alonso spanks Hamilton in Mclaren and vice versa at Ferrari. Different cars drive slightly differently with different strengths.
Vettel has so often shown a pace Webber can't match let alone beat, and rarely has the opposite happened.
Meh, sometimes I want to see a much more limited series with almost identical cars that puts almost all the difference in the hands of the drivers.
As you say, I don't think Button was ever even close to a great driver, I think almost any driver on the grid could have won the title in that car. I think Vettel is much better, because he can put his car on pole with much weaker showings in practice and a car without the lead the Brawn had, but ultimately if it wasn't Vettel it would have been Webber, or whoever was in his car.
This year might be the first year I really think the two best teams have been very close all year(race pace if not ultimate quali pace), just a real shame that Mclaren couldn't make that a real three way battle.
Still, a merrygo round of drivers would be entertaining and shake things up, but knowing how things work out, Hamilton would sign for Red Bull only to see Mclaren have the best car next season anyway