I'd definitely say the first one you posted is the most "authentic" looking and my favorite.
One thing that bothers me a bit is the outlines on the "button stripes". Since they're not repeated anywhere else in the design they stand out a bit. Maybe they could just be outlined in the background color. This will theoretically make them a bit more subdued and blend in with the rest of the panel more. I'm guessing you were going for emphasis, but the colored buttons alone are going to make them stand out a lot. I like only having the four colors used in the overlay. Outlining them in white might look really nice if some of the other elements (joy arrows, bars at top) used similar white outlines and lines. From what I remember, many of the Atari CPOs used a lot of outlines.
You might also try horizontally flipping the left "button stripes" so they're shooting up from the lower-left. This would isolate player 1's artwork to the left half of the CP.
The only other practical thing I worry about is if you allowed room in the design for dust washers for the joysticks. I don't know if you're planning on recessing them or not using them at all for that matter, but if they will be sitting on top they may cover the arrows a bit.
Most of the other designs have too many unrelated elements/colors or things going in too many directions. I think these make it look busier than it needs to be. They're all good parts, but together they just seem a bit much.
Altogether It's one of the best I've seen. Just thought I'd try to give some constructive criticism.