I haven't done any much needed re-arranging due to the TR line replacing some of my older TFs, but so far I've replaced almost all of the Hasbro FOC line with the Takara versions (Except for Air-Raid, prefer the Hasbro red) and sold most off.
Classics Bumblebee has been replaced by United Bee (shiny) which was then sort of replaced by TK Gen Gold Bee (United Bee was moved to my "extras" shelf, and might join my Neo G2 shelf as G2 Bee)
In fact a lot of bots have moved to that "extras" shelf - it's basically overflow from the Classics Autobot & Decepticon shelves, plus the current TR line for now, so I've got Classics Optimus with the FP trailer there while CW OP grew on me and is on the main shelf. Henkei Skyfire is also there while Gen Jetfire takes his spot up top.

But onto others I don't display at all anymore, that'd be the RTS (too cartoony) and United (floppy) Rodimus' while Henkei Rodimus takes their place (might be replaced by the TR version in the near future...) A KO Classics Ultra Magnus w/ FP armour is also no longer being displayed, as the Gen. version is perfect.

As for bots that I sold along with the FOC extras,
Gen Ultra Magnus, replaced by LG version.
RTS Perceptor and Gen Kup were replaced by the Asia Exclusive 3 pack versions (Shiny ,but new Perceptor looks cool too)
Generations Orion Pax, Bumblebee, Waspinator and Armada Starscream (replaced by Takara TG versions)
United Warpath (Replaced by Gen version)

And finally, I've got both the Hasbro and Takara versions of CW/UW Bruticus and Computron on display atm, still deciding which one of each to put away....