well no offense to randy, but that would make more sense. he had a choice of where to put the connector, and he chose to have it pointing into a group of buttons (if your doing two player or robotron style). i would have done it up, or even better, down. your almost never going to have buttons below the stick. maybe randy did think that this was best though, and it probably will never matter that much.
so don't get mad at me randy, or feel that you have to explain yourself. the most important thing is that it's not changing anytime soon, so it doesn't matter. 
Hehe. No reason for me to get mad, but I would like to give you an insight as to why I chose this orientation (I actually did think about it

)
There are 2 main reasons:
1) Even though space can sometimes be at a premium horizontally on a control panel, one can usually shift the buttons a half inch one way or the other to make things fit. There is usually a little dead space to the left of the the stick on most CP's because the stick is left of the buttons. On many classic cabs, the vertical space is very limited, sometimes 6" or less of usable space. So my thought was that placing it horizontally and to the left would offer the most flexibility to more people.
2) If you look at the function of the pins, they flow in a logical direction from top to bottom. +5, YA-YD,XA-XD and Ground. While this isn't particularly important functionwise, it appears to indicate that someone somewhere, perhaps the designer of the board, intended it to be in that orientation.
As for rotating the board, I understand that this will change the orientation of the mounting holes to properly fit a panel like the one shown, but the connector still needs to point left for proper operation. Or am I missing something (entirely possible)?
The other thing to keep in mind, if you really wanted to change the orientation, is that the controller, like any other, just puts out axis data, so you can correct for it in the controller setup for most applications.
RandyT