From the article:
For the origins of the ABXY button scheme we must look back to the very beginning of additional buttons. When the Famicom (known as the Nintendo Entertainment System outside Japan) launched, it featured two primary buttons. While other companies labelled their (usually two) buttons with numbering such as 1 and 2 or I and II, Nintendo had instead used A and B. When the SNES was released in Japan in 1990 they added X and Y to the mix, and rotated it slightly. The format was now a diamond, with X, A, B, and Y all around, clockwise. This format became known as ABXY because of the obvious alphabetical order.
But why X and Y? Why not C and D, the next most logical letters? The likely reason for this is future-proofing. Adding C and Z to the right of ABXY would not change the way games designed only for ABXY controlled, whereas if the controller had ABCD adding E and F and moving C up beside B would affect previous games, and having the buttons in ABECDF order would not make sense.
When Sony launched their now-standalone PlayStation in 1995 for US$299, it had its own take on the diamond: instead of letters it had symbols–a Circle, Cross, Square, and Triangle, respectively. They also added two additional triggers, introducing the typical ten-button scheme of many controllers.