Well I've owned Yamaha, Honda, Cat and Polaris.
Polaris 500 H.O. broke within one week of riding---tranny, and it would creep at idle. Rode great but was junk.
Cat bushings go out, drive-train is sloppy and it seemed like I replaced a lot of cv boots. Other than that my 500i manual could out pull, out mud and just plain out work anything I've owned. I rode that thing like I stole it for virtually 1,600 trouble free miles.
Yamaha was good machine except I kept getting water in tranny. It was a Kodiak 400 and was a solid machine. Motor started smoking at 1,000 mi.
Honda has the best fit/finish, handling and flat out reliability of anything I've owned---by far. I am talking about my Rubicon. 600mi
Polaris was bad but the most dissappointing machine has been my 2003 Rincon. When I rode in streams in the winter the tranny would stall out and leave me stranded in middle of creek. Water would get in motor all the time, airbox would be bone dry; don't know if it was getting through the exhaust or what. It was/is the best machine for trail riding but I don't do that. I guess a lot of it is my fault because I bought the wrong machine.