From what I've gathered, even with the 3.21 gears, 35s should be fine thanks to the 8 speed transmission. The 1st gear is low enough that it shouldn't feel sluggish. You may have a little bit of gear hunting at highway speeds with 35s, between gears 7 and 8. You can negate that by only allowing it to go into 7th gear with the gear limiter. Tbis also turns off the MDS. If I could go back and buy my tires again I would get 35s.
As far as the warranty, the Moss Magnuson act protects you. The dealer has to be able to prove that the modification caused the failure. Even then, the bigger lift companies warranty their product and your drivetrain if it is found out the lift does cause the problem. I dont know that I'll go with a 6" lift, but I will probably go with at least a 4" when more options are available.
Fuel economy is going to take a hit regardless. With 34s I can still get 18-19 on the highway. 35s I would imagine another 1-2 mpg drop. Ride quality should still be good. It will be stiffer but more so because of the stiffer tires than anything else. I've got 275/65 BFG KO2s and while it is a little rougher, it is not bad enough to bother me at all.