For instance, we designed the NKC "Freeduino" board to be slightly larger than the official Arduino (pushed the board to the left and had the connectors there hang less off the board, got rid of the "Italian Styling" on the right.) But it maintains the spacing of the important connectors, so it still works with most shields.
OTOH, other companies have built whole ecosystems around other board shapes. Like the Adafruit "Feather" and "Itsy Bitsy" boards, the "Lilypad" boards for wearable computing, and a slew of boards designed to use with 3d printers than have an Arduino-programmable core, plus room for a bunch of motor drivers and such.