I'd be interested to know how many people making those comments actually have an 04 Axiom, or even for those that do, how many have put 110K miles on one and are now at a pretty high mileage (almost 185K for us). I find a lot of groupthink goes on in message boards where people with no experience often parrot things other people have written. Not a big deal, heck I've done it myself too, BUT the problem is when people don't admit to having no direct experience.
The engine is newer, but if that's your only criteria everyone would have traded in their first-gen Mustangs and Corvettes for Pintos. The new engine shares very few mechanical bits with the exponentially more available non-DI 3.5 and 3.2 engines, and it has a much lower tolerance for non-premium/detergent-enriched gasoline (lots of people have multiple $300+ OEM injectors go bad in the 100-150K range which is just ridiculous). People will also tell you that they don't burn oil because of the new piston design but that hasn't been my experience at all - it's been burning as fast or faster than my VX since we bought it at 72K miles.
They are right on the transmission being different than in previous years, including 02 and 03. When Buffy did my 5-speed swap I called Merlin to see if I should keep the auto as a back-up for the Axiom and he said the part number was different not only from the VX and Trooper transmissions but also from the 02 and 03 Axiom transmissions as well. They're all 4L30E variants, but some change must have been made along the way. What that change was, and how significant it was, are anybody's guess. Maybe Jerry Lemond would know?
Again I'll caveat all that with the fact that we've thoroughly enjoyed owning it, especially my wife who drives it every day and believes it is unkillable (largely due to those accident survivals I mentioned). It is a tough little SUV, but I just don't want you to jump in blindly thinking that it will be significantly more reliable than your VX.