I concur with what others have said. If you are building this arcade with the intention of just you and your wife solely playing it, then great, whatever works best for you. If you have friends who will be coming over and playing with you, like at all, then I would reconsider your layout. I just know that I couldn't handle the wrong sided joystick. And even other lefties might not like it too. When you go to a real arcade, they don't pander to lefties either. So they likely have been using "righty" controllers all their life. So I would think that this would even feel weird to them. If they've never played video games before, well then I guess it's fine too.
If you placed the controls in this way simply for aesthetic reasons, or for symmetry you should definitely reconsider. You can still achieve a very clean symmetric look without flip flopping the buttons like that. I attached a picture of my control panel. The controls are symetric, even though the joysticks are on the same sides.
I would have to agree with others on the golden tee / bowling comments as well. That's the one regret of my control panel is that I put the exit button at the top, above the track ball. So when I give the trackball a good push, I have to pay attention to not hit the button and accidentally exit the game. In your case, they might stub their fingers on other controls that are on top. If you have the trackball there just for games like centipede and etc, then maybe it will be ok, but even still. I find it's best to plan ahead just in case down the road you want to play these other games.
The big piece of advice that I give to everyone, and I can't stress this enough. BUILD A TEST CONTROL PANEL. It doesn't matter if you use ply wood, card board, whatever. Just build it and play a few games with it. If the controls are uncomfortable, it should be apparently pretty quickly.
With control panels it's a very personal thing. So if you're pleased with how this CP operates as you have it currently laid out, then go for it!