My first CP was like yours with the joy on the right and buttons on the left on one side and the opposite on the other side. My kids told me that they wanted to play with their right hands on the joystick and hitting buttons with the left so I'm doing it that way.
Early machines often had the joy on the right and a button on the left or had a button on each side. Later, hitting the buttons was more important (at times) than the joystick direction so CPs adapted.
I'm guessing that most people have a preference based on what games they played the most growing up And those much younger than us are probably more adept at using either hand for buttons since they are on various phones/handheld games/tablets much more than we were at their ages.
And don't worry about people here liking what you did. If you like it, great. If not, change it until you do. 
thanks man, yeah im not taking it to hart, i did wanted to hear some comments even if they are bad.
me and my friends, we are in our early 30's and so far the reactions varies...
me myself i was ok with the joystick been on the right but then the configuration of buttons i preferred to be left to right vs. right to left.
ill give it another month or so to see how people react and then decide to change it or to let it be.
i got enough headache with the software and the hardware questions this days.
with the 3D games not working well at all.
i think my dual core amd been 2.4ghz is not enough for the Tekken and die hard
and i haven't even tried the ps2 emulator.

im thinking of a quad core with 4gb ram and an ATI Radeon HD4670 1GB hopping that will do the trick.
any suggestions anyone?