I have the GTX in mine. It sticks out into the upper HDD bay, partially blocking one of the places you could put a hard drive, but thats not a big deal because there's still 5 spaces left. As for the wires, I zip tied as many together as I could, the rest I stuffed into the small compartment below the bottom HDD bay, thus the air flow is only blocked by the bundle of wires I have zipped togehter, so it's minimum blockage really. I also was able to route a few cable behind the mobo tray without any modding at all, because there were already a few places you could route wires through.
However I hate the fact that the CPU power supply cable just barely reaches without having to route it directly over the motherboard.