Well, I have no problem using Both, However I do generally use X more than Y. You can put your thumb on both X and A, just like you can put your thumb on both Y and A. I don't think Y's placement is an advantage over X's placement.
Customizing controls would be cool and and make many people happy. However this would mean that every time you go to your friend's house, a tourney or change controller ports, you would have to check and make sure your controls are set the way you want them. This could be annoying and time-consuming.