I think it would have to be a decision based on personal preference and the functionality and main use which you're looking at.
I own and am currently using a Mini 9, which I respectively chose over all the other notebooks available due to good reviews, decent price and ability to upgrade the system. Screen and keyboard were not too
small for me (note: the right shift key and '?' is tiny, takes a little getting used to at first".
Obviously the Mini 12 is bigger, not sure myself but think it's more powerful with a larger hard drive. I am personally not sure whether at this point I would choose a 12 or 9 if I had to decide, as although they are both small in size, the extra power could come into use, but the portability of the mini 9 is astounding. Fits into my bag for college, along with other folders, bits and bobs very easily indeed. Not too sure if the same can be said for the 12 but from what I've seen it's still a pretty small laptop.
From what I've gathered you won't be able to go higher than 1Gb ram in the 12 which could factor in if you want to do anything particularly CPU intensive.
If I were you I would probably go with the Mini 12 in the end - the larger keyboard, processing power and screen could come in handy and still be a very portable, yet capable laptop (sorry not sure about the price of it though!). Still the decision is yours. Hope I've been some kind of help.