First off, great question.
Now, I don't think anyone really knows. But my theory is that it reflects the two legendaries Xerneas and Yveltal, as Xerneas is life, or a new *beginning*... A. Yveltal is death, or the eternal *end*... Z. And I think it is extremely possible the names for Omega Ruby and Alpha Sapphire were devised early and his name reflects this.