I would lay your hands on a sheet of paper, in playing position, and mark your index, middle, and ring fingers, in addition to your thumb.
THAT is where your buttons should be for maximum comfort/playability.
What you will probably end up with is a Neo-Geo layout.
The Neo-Geo layout will let you play all 1, 2, 3 and 4 button games comfortably, except for Vanguard--which is the only game that requires the diamond pattern.
Neither of the two layouts you proposed will let you play 3-button games comfortably.