I play 12 string guitar and use MG2 for live gigs - it is simply fantastic! I use it to add strings, organs, flutes and choirs as backing. However, MG2 operation with a 12 string is not as good with as with a 6 string and the fundamental reason seems to be that MG2 can only keep account of 6 output ‘streams’ at a time, and of course there are 12 strings on a 12 string guitar (duh! 
). What happens when you play a down-strumming chord on a 12 string is that MG sends notes in the sequence they are hit, but as you go beyond the first 3 octave pairs and hit the fourth (G) cotave set, then it stops the lower first played strings and replaces the outputs with the higher strings. So the lower string voices quickly get cut off. I can see that adding more parallel ‘streams’ might take up more processing power, and become difficult for some processors. However, I don’t think that MG has to have a full 12 stream output, as there are many duplicated notes on a 12 string. It would appear that MG simply resends a duplicated not (ie the top unison B’s and E’s) without giving up a place. So my suggestion would be to add support in MG for an selectable number of outputs, say up to 9 or 10 outputs at a time, which would cover most simple chords on the 12 string (I think for example, there are only 8 unique notes in a straight D chord, 9 for a D7). I don’t know if that would make things very difficult, but it would really be a great feature for 12 string players.
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We haven’t looked into tracking 12-string guitars yet, and it will always pose a challenge with the octaves, but I have in on the to investigate list, for after the MG3 release.
12 stings are strung two ways, one with the octave string on the top (Rickenbacker) and with the octave string on the bottom (Gibson).
I assume having a selection available in the set up menu would help make tracking easier. I’m a big believer in using items in the setup menu to help make tracking more accurate.