Well people in English (and probably most non-Asian)speaking cultures read left to right and top to bottom. This makes the top left corner a natural reaction for anybody that has never played your machine before.
In addition, you would have to reprogram any game with more than 3 buttons if you want it to feel right. I would go with:
123
456
However, using NeoGeo buttons configurations would complicate this, but I don't see you using one. You could probably make it work by lebeling it well if you decided to put the 1,2,3 on the bottom, but then it would just confuse people when they try to play games with more than 3 buttons cuz then everything would be reversed, anyways.