Hardest Elite 4 would probably be the Sinnoh region's. They were brutally beating me, especially starting with Flint since I had no Fire Pokemon. Cynthia was pretty challenging as well, but not as much as Steven Stone.
I guess sinnohs but ONLY because I think they outleveled me by like 15 levels while other games they would only outlevel me like 5 levels.
Really any of them are easy with spending some time to train your Pokemon.
Cynthia's Garchomp was difficult for me, but the hardest would have to be Ruby. Not Sapphire. It was easy in Sapphire because Kyogre was epic. But Groudon...Just isn't good there.