does anyone consider the Mac Mini to be too big?
No, not at all, it's an incredible little package, no need for it to be any smaller, that's what an Apple TV is for...I hope the Mini retains its current form factor because I like that as shipped it brings so much to the table, and I don't want to lose the space inside for two drives of my own choosing...
the NUC kit I looked at on newegg.com had considerably less ports and an external brick power supply.
Agreed, if Apple goes Haswell NUC it would be with something customized. But, as you'll probably figure out once you get your Mini up and running, its fan does present a minor inconvenience, it's intake is on the bottom, so most of us elevate our Minis a bit, and dust and gunk does get stuck at the metal mesh just inside the black bottom disc. Now imagine the same Mini with greater processing power without any need for a fan? That would be a very elegant, very Apple-like evolution.
I just bought an open box 2012 base Mac Mini and haven't configured it yet, but I was under the impression that for most HTPC purposes the fan probably shouldn't even kick on.
Who gave you that impression, not someone in this forum I hope? The fan most definitely revs up with a 2011 or 2012 Mini when doing something intensive like a Handbrake transcode or playing back a blu-ray, two things one would do with an HTPC quite often. But, whether you'll even hear that over ambient room noise sitting 10 feet away, I doubt. I don't ever hear mine over and above the most quiet of passages, (and I even turn my fan speeds up a little bit on purpose just to keep the Mini as cool as possible.)
but I doubt a NUC would be a good platform as a transcoding server.
A Haswell NUC? Haswell is supposed to be a significant step up from Ivy Bridge, where Ivy Bridge (2012 Mini) was just an iterative step up from Sandy Bridge (2011 Mini.) Haswell should do a killer job transcoding media, but, I think what you'll find is that your 2012 Mini will probably already be overkill for your HTPC needs, it'll do live transcodes just fine, barely breaking a sweat.