Got one of these for some time now and as mentioned in the review, exactly the same issues I had encountered with the PSU and GPU meeting up in addition to the massive concentration of wires.
I am planning to reduce the amount of wires used though via removing all Internal HDDs and relying on an mSATA SSD for the OS. I was also thinking about moving to the SFF PSU that Silverstone released but, my current PSU (AX750) is still pretty recent and fully functionally so shelved those plans.
The issue I do have at the moment is that the cooling profile seems to be bizarre, not sure if it is the fans, or how they are currently connected (all into my mobo at various ports, kind of sucks as I am using the PWR_FAN port due to the location for one of them

) which to that end, getting some Noctua NF-12 fans to see if they will have any impact on cooling performance.
A fan controller would be nice but I would have to re-introduce a MOLEX power cable back into the case so going to avoid if I can.
The only two others thing I am considering, as mentioned in the review, is a motherboard that lets me use the top PCI-E slot for graphics so I can claim some room near the PSU back or considering a mini GPU card.
The whole reverse fan thing is still odd to me but, going to install some extra fans in the roof and maybe the bottom to see what happens. (hopefully I remember the fans are inverted and any extra fans need to be installed with that fact taken into account) As for water cooling, something for the future!