Yes, the top should match the bottom in terms of layer-order.
I'm not too keen on the rounded edges, mainly because the bottom one reminds me of hotdog weiners...and someone squishing the middle of them. I understand that your CP is rounded, but those bottom bars really look strange, especially that bend in the middle. Personally I'd make the everything but the edges (if you are set on retaining the rounded nubs) angular. I'm talking about that bend, specifically. Either that, or just keep the bars straight and have them traverse under the Space Invader, but he can have a black outline around him to separate him from the bars.
I would also continue the top bars throughout the buttons, or you can do what I mentioned with the SI guy, have the button holes have a black outline around them, separating them from the continuous line across the top.
The rose-dials around the joysticks definitely need more refinement. I would make the arrows much smaller, separating them from overlapping. Try to get some of the black between each arrow. I'm not sure why you put that middle part in, it's just going to be cut out from the joystick hole.
Overall, the whole image just seems too plain, and there is a lot of negative space not being utilized.
The retro art-style doesn't mean just straight --simplicity--. You still have to put some cleverness into it, whether it be from contrasting proportions of the visual elements, adding some design "textures" to it (aka patterns) or just adding more complimentary colours for some more visual depth. Stepped-gradients are also good to add for some visual stimulus.
Your colour scheme could also use a few more additions, perhaps one or two neutral half-way colour like a brown or grey (used sparingly of course) , and maybe another main colour.