In the beginning, I'd say Gen 1 was definitely more difficult for me.
Brock- pretty simple if I got Bulbasaur, but I generally got Squirtle. And Brock was absolute hell if you got Charmander. (Bulbasaur would have Vine Whip and Leech Seed. Squirtle would have nothing but a measly Bubble, which made it much easier to beat Brock with Bulbasaur even if they both have an advantage.)
Misty- She was particularly hard in FireRed. Her Starmie knew Water Pulse, which constantly confused my Pikachu. I don't even remember if she was hard in the originals or not.
Lt. Surge- His Raichu was sure a challenge for my little Pika and Wartortle! His Raichu was just very fast, and I remember having to save before I battled him so I could restart when I lost to re-challenge him.
Falkner- I usually got Cyndaquil, and Falkner was a breeze. I recall having a Chikortia and having difficulty beating Falkner because of Mud-slap.
Bugsy- Again, with Cyndaquil, Bugsy was a piece of cake.
Whitney- I know a lot of people had trouble with Miltank. I got a female starter and had a female Flaaffy with me. Miltanks lady-charms were no match. In SS, Milk Drink caused a small problem, but I believe I still beat her first try.
So yeah, at the beginning, Kanto was harder for me. But later on as I developed a strong team, both were fairly medium-difficulty. I don't remember having to rebattle any, I think maybe I did with Claire? I don't know.
I'm surprised not many people had trouble with Lenora from BW, I had ditched my starter and she gave me a hard time.