I think the biggest question here is... how many actually cares about the continuity between CMI and up to Tales?
Personally, they might as well be completely independant for all I care. The continuity between them was already somewhat derailed on CMI (but not so much noticable that I cared alot about it), EMI basically messed it up completely (at least, I don't agree with the way it took), and Tales almost ignored everything that had happened since... well, since E'n'G got married. I simply don't care about the continuity anymore, hence why I wouldn't mind a MI3a. That's also why I always thought a series called Memoirs of Guybrush Threepwood would work - forget about the continuity. Just make individual games with a couple of references here and there, but don't make permanent changes. Tales did this pretty well, and that's probably why some people (me not included) think it's the best in the series (crazy people).