We have built a lot of Shuttles for clients with "Designer" offices and in most respects I cannot fault them. The build quality is excellent and so far looking through my fault logs I see only one hardware failure (a dead PSU) out of circa 30 machines over 3 years.
The shuttle kits look a little expensive until you realise that you are only needing to add Memory/CPU and drives. The only limitation I would say is that you only get one PCI and one PCI-E slot so expansion is a bit limited and you are also restricted on the physical size of any gamers graphics card you may want to fit.
However they generally come with a good selection of interfaces and integrated peripherals so that isn't always so much of a problem for a good general purpose pc/light gamers machine. Given the built in stuff they have I can't think of many PCI boards the average user would need to add.
ASUS and a few others do something very similar to the shuttle kits but in my experience they are not in the same league when it comes to build quality and reliability. It's different from what you are looking at where you can fit a generic mainboard..Shuttle and the Asus machines use a special format mainboard.
It might be a slightly less flexible solution than a case like the one you are looking at that that uses a generic mainboard, but what you lose on the upgrade path I think you gain with things like more effective cooling and efficient layout due to the board being designed around the case rather than a case designed to accommodate a board.