Metroid Fusion.
So many people were against the idea of it having a narrative, telling you where to go, and Samus talks
But who cares it was a fantastic game
As for RSE - I believe a lot of complaints were because of how they ditched the connectivity with previous gens - making the game have only 202 out of 386 possible Pokemon to catch - meaning only 67 of the previous 251 were obtainable
"Classics" like the RBY starters were not obtainable at all
Of course, the release of FRLG fixed this, so it was no longer a problem after that