Theres only really one reason to go with a full pc, pci/pcix slots
if you need them then go for a tower, the shuttle is pretty good for everything else, definately check if your chosen GFX card will fit but the SN25P should take a double thickness card, you can get 3 drives in there without any hassle (just make sure you stick to sata and buy your own sata cables) and temperatures honestly aint bad, i remember using the drives i have in a previous shuttle & tower system and having to allow them to cool off before handling them, the P series seems to have fixed this they are just warm to the touch
the only other thing id warn about is that it'll make a future cpu upgrade expensive, normally for a new socket your talking new cpu + mobo + ram but if you have to switch to a new shuttle it'll bump that cost up significantly. id look into the shelflife of the 939 processor because i heard something about them extending the life of 754 and dropping 939 in favour of AM2/AM3 which royally sucks since 939 was to replace 754