Stoney,
How about a reply from someone with absolutely NO brand loyaly as I have never owned an ATV. I have been researching them off and on for a few years, lurking and posting questions of a couple of ATV forums.
My take on this is exactly what many others have stated: the field has pretty much leveled over recent years amongst the various brands. There are some differences, but most, on average, are pretty good machines. I agree with those who stated that Polaris may have some quality control issues and they do require more maintenance. I just went ATV shopping today and it was hard to keep my eyes off the Polaris models - they are good looking rigs. But my opinion of them is tainted based upon much reading on the forums.
I think another generalization that has been made on the ATV sites is that early on, Honda did enjoy a reputation for above average reliability. This has been repeated many times in this thread. My understanding is that today, the Honda isn't really much better than the others because the others have gotten better (more reliable) recently. Hondas are characterized by many as having a stiff ride. This would be a significant issue for me as I'm getting older. Bikes with independant rear suspension are much kinder to those of us with aging bones, so I'm told. The young bucks often like the straight axel so they can "power slide" through turns and they might be a little faster out of the gate. These issues rank very low to me. As was mentioned, Honda has been resistant to changing their rear brake from a drum to disk. This seems to be important to some folks.
Another truism I have learned is that some bikes from all brands will be lemons. When that happens, the owner goes to the forums and states what a piece of junk it is and that they will never buy that brand again. Or they have a friend with brand x and has had nothing but problems so no one should ever buy that brand.
But, just like you hear (read) on TBN about tractors, one thing that is universally agreed upon is find a great dealer first, then buy something he sells. If you do have problems, they will take care of you. I can't tell you how many times I have read a post from a disgruntled ATV owner who took their bike in for warranty work and left cursing the dealer because they attributed the problem to abuse of the vehicle. HELLO!!! These are off road machines. Their own advertisements show them going through mud holes, climbing rocks, etc. Don't know how they define abuse. But, with a good dealer, this would not be an issue.
This brings me to my last point (which is repeating another poster). While you can save substantial money buying used, personally I would avoid doing so unless I knew the seller well and knew how they used their machine. On the ATV forums I read what some of these knuckleheads are doing with their ATVs. No way would I want to assume the risk of buying one that has been used like many of these are used. Should I decide to buy one, whoever buys it from me when I decide to sell it will get a great deal as all I intend to do is putter around following my kids or taking some leisurely trail rides. No mud boggin or rock climbing or flying through the air for me.
Good luck with your decision.