Couple of points here;
First, regarding MT or AT, that's like asking what the best color is for a Jeep. It's very biased and depends on taste. Personally, I like the manual, but others prefer the auto. Neither one is "better", and both have pros and cons. Other than that, I doubt the AX-5 will last long behind an I6... Which is why I6's came with the AX-15. and IIRC, the input shafts of the two are different anyway, so you need to make modifications to make it fit.
Second, if you are going to do an engine swap to an I6, I would recommend selling the Jeep and buying one with the I6 stock, then transfer all the goodies from the old Jeep to the new one. You will save time and headaches. If you are gonna do the engine swap (even if my understanding that the I6 you are getting for free), you may as well go for a V6 or bigger... It's the same amount of work. Or get a turbo and install it to the I4, and you'll probably spend less than the engine swap and have more or less the same power (probably a bit less, but less weight as well).
