I can't think of anything currently, not that that has anything to do with anything. I suppose the old BGS as opposed to the new BGS could be considered. There maybe some others, but I just try to adapt to any changes that come my way and try not to think about them much.
I too continue to play, I have also 'adapted' to the new discovery process, the 'I'm alright Jack' stance is not a useful argument against the retention/reinstatement of the old functionality.
I play the BGS, manipulating minor NPC factions alone in a relatively quiet region on space, and bugs aside I have not seen any change that does not allow my to continue as I always have. It is a new interface with some changes to rules & trigger points (some of which may still be bugged - the triggers for famine or retreat for example) but no gameplay has been removed, the changes are justified as far as I can see.
The Crime/Punishment changes in 3.0 put in a lot of new features that many players hoped would stamp out certain playstyles (aspects of PvP) but all roles are still possible, some now have busywork (visiting an interstellar factor comes to mind) but again, the changes were justified by FDev. For the ADS (the most powerful of the old modules) there was no justification, no need to remove them.