I think I prefer the top one because the buttons are symmetric; however, I'm not against the idea of asymmetric buttons if
they are implemented in a fashion that makes sense. Currently, the way you have your GUI arranged they don't make efficient use of the room or warrant their strange shape. If you were to redesign the gui to look more like a computer panel with different-sized buttons then I think that would be fine so long as the buttons are all large enough to identify and click on.
I do like your existing GUI design overall, though, so I think you should consider going with symmetrical buttons for it, that way you can make more efficient use of the space which should be a design consideration, like so:
1. Redesigned the buttons to stand out more and to better conform with the shape of the gui and for efficiency while still leaving room for effects.
2. Made the close button slightly smaller (may or may not need one at all but it's a good way to show some functionality).
You may or may not want the buttons to look like physical buttons; while I like the idea of virtual buttons, as Frito Master pointed out you are going to want to make the buttons more obvious (which is what I did). As you can see, I've made more efficient use of the space while still leaving ample room for flashy stuff. In this case, I thought it might be cool to add some digital marks next to each button that would light up when you mouse over the button (4 is lit in this case). This adds more visuals to the interface without cluttering it up, but you could also remove the center area and add even more buttons if you wanted. As it stands, the gui will support at least 6 buttons and they could all be symmetrical if you either reduced their heights by 1 pixel or the size of the surrounding gui arch.
Hopefully this helps and take this opportunity to really experiment with guis. While a clean, easy to figure out design is extremely important, you can still have a lot of fun being creative with various aspects of the design, especially with futuristic or steampunk stuff where your imagination is the only bottleneck!