If you are using a window in the case, no matter what you do the motherboard and CPU fan are the largest things that will make the interior look bad. You don't really have anything that bad with the cables, they look to be pretty much the shortest distance and with no space between the motherboard and top you can't route things closer to there so you will have cables across the motherboard. Either way, the motherboard kills anything else you try to do, you are putting lipstick on a pig here.
My case is about the same size and I used the large area to put in some decoration inside it to take up the empty space, the difference is your green motherboard, cooler and case design pretty much take away from anything else you may do to your case, you are adding more to the case not making it look better, the whole thing needs to tie together, adding things won't fix the existing issues or make them look nicer. Instead of spending money on a water cooler I would get a standard motherboard and nice heatsink/fan for the CPU and stick some things you like in the case along with sleved cables to match your color scheme.
For my system the next couple of things I will be doing is maybe installing my AIO on the front to cover the large blank hole and replace the stock fan, and a back-plate for the video card. I did not really want to install the AIO water cooler on the front to keep the intake from being warmed air but my motherboard RAM is blocked a bit by the cooler up top.