Straddle your bike and look down. You'll find that your right peg is further forward than the left. Could be a factor in your lack of joy in the peg placement, as well. Kinda feels funky in a way you can't put your finger on because the stagger isn't obvious unless it's pointed out, but it's close to an inch.
The 6-speed and 25 more cc's could have been done at any point with existing XT and TTR parts already in production. I'd be dazzled with that, but even when Yamaha did produce a TW225 for the Japanese market they stuck with the 5-speed. Go figger.
There is mucho wrong with this bike but most of it is correctable. Be careful what you wish for, or Yamaha will build it in the image of their XTW250 concept bike, which is built in the image of a Super Tenere, and so on.
Flavor of the week. Wrong way to go, but they may take it there. We'll see.