It isn't necessarly that one is better that the other.... Having owned both, I prefer SFF (Small Form Factor) PC's. They require no special hardware, as (most) come as barebones systems that already have the motherboard, PSU, and (not sure how many) with CPU coolers.
My shuttle (listed in sig) is CONSIDERABLY smaller than my full tower, and has about the same foot print. Also, there is room for 1 optical drive (no need at all for 2 IMO, even when copying disc's), and space for 2 HDD's, and 1 FDD (if you still use them, not much point anymore) / 1 additional HDD. Depending on the model you get, there are various expansion cards... Mine is limited, I have since PCI-Express x16, and PCI-Express x1..... no legacy PCI slots, not that I need them, as audio & LAN are built in, and there is also a header on the Mobo and a mount on the back of the case for a WiFi antenna.
A full tower would be good to have as a server on your lan with the additional HDD's you may need... I would again prefer a smaller NAS box though, as it would consume less power.