The question of how/where to tune the 12-string depends somewhat on what you're going to be doing with it. For example,
Down a whole tone (2 frets) and C standard is your D ... but E = F# (ouch) Down 3 frets, C = Eb (ouch again), but E = G (yay!) Down 4 frets, C = E (yay!), but G = B (yecch)
See what I'm getting at? For some keys, it's an easy transposition, for other keys, it's a pain. With a capo, of course, you can overcome these problems, but you introduce the out-of-tuneness that comes with capoed 12-strings (and no, I've never heard a single acoustic 12-string guitar that would capo perfectly for more than three or four frets... not a one... really... well, if you know of one, send it to me and I'll play it a year and tell you if I like it).
De-tuning and transposing are part of the game with 12s, and that's the nature of the beast. Tuning to standard sacrifices part of the inherent quality of the 12-string sound, but makes transposing as easy as on a six-string. Tuning low makes transposing more of a nightmare, but the sound! The sound!
If I ever get another 12-string (I just bought a boo-teeky guitar, so another one -- soon -- is out of the question) I'll tune it low and live with it. And whether it's two frets, three frets, four or even five frets low will depend on the sound and the amount of transposing I want to be subjected to.