They are completely ass backwards and wrong.

Tried setting it up with 360 controller and my Qanba Q4RAF

It thinks the buttons are swapped around. It took me a while to set them up blindly but why?

There's a separate button config executable, look for it on the start menu.

think this game was 1st made for the psp. could be due to bad porting?

Actually the GG series started on the PS1 and the games that are on the PSP are also available on PS2 , PC and so on. Not to mention the PSP ports were released much later than the PC version of the games.
As far as controls go , there is nothing wrong with them. They're just intricate.

My controller was all weird and not recognizing the start button, until I switched to DirectInput mode on my Logitech F710, then it works perfectly.

I have no problems with the controls because I'm one of those people who never bought an XInput controller and always stuck to a DirectInput one from before the Xbox controller became popular for PC ports.