+1 CarPlay (biggest thing here for me is text message integration, music and podcasts would be nice - but staying productive while on a long drive is huge)
Ability to add lumber/ladder rack. I frequently need to haul 10 to 16' material. It just not possible with the R1T without a flat bed trailer.
+1 on cab organization. The cubby under the drivers seat isn't a substitute for the missing glove box
Fold down rear seats. I miss the ability to create a flat surface for storage in the rear seat area. The gear tunnel is great, but not big enough for stuff like a miter saw
Obvious by my comments - I'm using my R1T as a work truck, not an adventure vehicle. (Somebody's gotta pay for this toy

. )
All that said - I do miss my F-150 - but wouldn't go back to it on a bet. The pros - way out weigh the cons. To everyone that asks me if I like my truck (at least once a day I get that question). My standard response is "it was worth the 3.5 year wait and I'd wait again if I had too"