The shuttle PC you described would not be the same size as a mini. Two full size TV tuners and a full-size hard drive would not all fit in a 6.5x.6.5" anything, let alone being 2 or even 3" thick.
As an HTPC, yes, I agree that a mini ITX form factor is superior and much more flexible than a mini. But getting one that looks good and comes with all the incidental features costs as much as a new 15" PowerBook. I've been pricing them out for months, trying to assemble a small, nearly silent, and powerful MythTV box. So for aesthetics and value, a Mac mini with a tuner add-on would be much better. Especially with the Front Row interface (which is much more refined and smooth than any Linux frontend).
Right now I use the same box as my actual PC (an Antec Sonata case), and simply worked Myth into my Linux distro. It works phenomenally, but I want to take advantage of a separate machine so I can use my monitor's Picture in Picture.