I don't mind the PlayStation button layout, but I do have an issue switching back and forth between the different ABXY layouts for Nintendo and Microsoft.
Besides the N64 controller (which doesn't have XY buttons anyway), which of Nintendos controllers had a different layout for ABXY?
The GameCube had the A button at the bottom/middle, B on the left, Y on top and X on the right.
SNES/DS/3DS/Classic Controller/Wii U have the B at the bottom, Y on the left, X on top, and A on the right.
Microsoft puts A at the botton, X on the left, Y on top and B to the right.
Usually I adjust fairly quickly, but for something like Madden or FIFA where I play on both 360 and Wii U it can be annoying.