One of the main things to be concerned about on the Ultra, particularly if you do any two up touring, is the load rating on the tire. Putting an 18 on the front would not be a big issue, as there are 18" tires available that are the same load rating as the 17". BUT, other than the 18" tire made for HD by Dunlop that fit on the '11 SERGU and likely the SESG with 18" rear, I don't know of another 18" rear tire that is rated for the loads you'll see on a touring bike, if you use it for touring. The 18" rear is not even listed on Dunlop's website the last time I looked...only available at HD dealers.
And yes, there is always going to be a bit more sidewall flex in a tire that has a larger/taller sidewall, so there would be some small difference in ride quality.
The rear tire on a Ultra, with two bags, a TP, and likely a piece of luggage on the rack...plus a passenger of whatever size/weight, it generally technically overloaded anyway by most folks, so if you start lowering the load rating, it could be a bad thing at some point...