DEFINATELY go for the 650. The $1000.00 is money well spent and the gap closes when you realize a speedo will cost you extra on the 360. As far as longevity goes. I have 3500 miles on my prarie 400 and my dad has 4200+ miles on his prarie 300. Both are starting to show signs of needing some cvt attention. But don't fool yourself Mr. shooter, any cvt driven quad will require more maintance than a standard shift once the miles stack up.
In the 3500 miles I have only had to replace brake shoes(3x) and one belt on the cvt. My dads 300- same thing.

If you want a honda, get a honda. Or the first time you have to adjust the air pressure in the tires you'll be saying "man I should have got a honda". But I assure your they're not all bullet proof and each brand has it's issues. Their is no perfect quad made.
Don't rule out looking at the suzuki eiger. It is a 400 class auto with a low price tag.

And Mr. shooter- the mighty 450 kodiak is only a 421cc motor-check the specs
Good luck on your choice.