Remove: Girl
Replace: Twist and Shout
6 songs from Rubber Soul is a bit much (especially compared to the 2 from Revolver), and although I would consider just about every song on the compilation a classic, "Girl" doesn't stand out as an essential piece.
There are so many other songs that could easily work in this set. It makes me wonder why they didn't make it 14 songs per disc, like the 1967-1970 counterpart, especially since the earlier songs are shorter, and take up less space.
I went with "Twist and Shout," as it seems to be the most recognizable song missing. I am aware that they purposely chose to exclude cover versions of songs, so my next option would be "I Saw Her Standing There." However, it is a real pity there isn't more Revolver being represented. But the problem with choosing a song from that album is that they seem to be all equally worthy of being included. But I would side more with either "Here, There and Everywhere" (one of Lennon's favourites AND one of McCartney's favourites), "Got to Get You Into My Life" (a top ten hit/most recognizable?), or "Tomorrow Never Knows" (the critics' and fans' favourite).