The money you are spending is on the electronics. And I don't care what kit you get, I HIGHLY suggest that you get good electronics. such as the DS615's and DS655 servos. I would also suggest that you invest in either an AR7200BX or an Ikon as they are some of the best gyros on the market right now with a decent price. You can find kits on ebay without gyros and save yourself a little money.
When I did some shopping, I added up all of the servos, ESC, Motor, bec and other items, and found out that by getting a supercombo, you are pretty much getting the kit for free. Just something to think about.
And yes, I think it makes that kind of a difference. Align is MUCH better than the clones that are out there.