Good points. I want the add-ons of the Rally because I plan to use it on a 10,000 mile trip this summer with two or three thousand miles of dirt and pot holes plus the odd stretch that the standard bike won't make without a fuel bowser.
My impression of size is that, apart from the Rally being a tad taller, there's very little difference between the two bikes, if you remove the boxes and bars from the Rally. I was surprised by the almost imperceptible difference in bulk around the tank, given how different GS and GSA have always been. Almost all of the increased fuel capacity is dealt with by the switch from a double-skinned plastic tank to a single-skinned steel one. That said, of course you are, at times, carrying 8 lites of additional fuel relatively high up.
IMHO Pikes Peak is the wrong MTS for 99% of riders (and probably the majority of PP owners too). The average PP buyer falls for the Ohlins thingy plus a paint job and ignores the fact that V4's superpower isn't really the fabulous engine, the superb chassis or the German-bashing build quality. It's the extraordinary ability of the SkyHook suspension to reduce the average UK road to racetrack smoothness.
Is your view about loss of agility/handling etc. based on experience or prejudice/expectation/assumption?