Oh lastly the drive cage in the Lian Li Case can be removed which is what I would do to increase the cooling effect of the front fan. Instead of cramming the case full of HDD which would be better served in a proper nas box or Windows Home Server.
I'll reply to this one other than wall-of-text quoting..
The motherboard can hold a discrete GPU! It's all about the case.
BitFenix Prodigy would fit nicely, but those Lian Li's sure are sexy.
SilverStone also make some incredible ITX chassis like the FT03 that would house a GPU with no issues.
I just got done playing around with an ASUS P8Z77-V PRO, but I use an ASRock Extreme6 for day-to-day. Very similar boards - I prefer the ASRock though, for one of the reasons you list above: mSATA. I also prefer the fact the ASRock has a debug LED whereas the ASUS has the phase LEDs.