Why would anyone want analog sticks that are staggered? That was one of my biggest issues with the Xbox 360 controller. The other is the massive size.
I don't like it that way either, but many prefer it.
You know what would be awesome? Having the ability to use either controller on either system. Probably not feasible really outside of clones or extreme modders (and with things like touchscreen, perhaps never), but it would give you the ability to use your favored controller in all things.
I have a real Genesis MK1, but also a clone that lets me play Genesis games using a SNES controller. I also have an NES to Gamecube controller adapter that lets me play the Gameboy adapter games (to be compliant with Twin Galaxies rules for Gameboy games), as well as a PS2 to Gamecube controller adapter (so I don't ever have to use the atrocious Gamecube controller).
The thing about controllers is almost like music. Person to person, you will never fully agree on how they feel/work for you individually. Some people say the NES controller hurts your hand, I love them and never feel any problems with them. Some people say the PS3 sticks are too close, I never had any problem with them. Some people love the analog sticks on the Xbox controllers, while I don't really like their feel. Etc. There's not really a 'wrong' answer, unless it's something obviously ludicrous like the Jaguar or Master System controllers.