If I am not mistaken Hoenn was considered the most difficult of all generations entirely due to the fact that the first Gym through third Gym more or less destroyed you no matter what Starter Pokemon you had chosen. As well as the fact Winona had a legitimate "NERF" from the games that shipped at launch, and those that shipped about 6-Months Afterward; the original cartridges to this day sell for more since that adorable Miltank kept on Rolling, and Rolling, and Rolling the Sanity away from Players due to the shear about of damage output and speed.
This being said, my personal opinion, is that the Kanto Gyms were the hardest as this was the first generation, before most people knew what made a proper "Gym Team" and people went in with their favorites. It also followed the Hoenn Model of a Rock Starter (Required Water) and then immediately afterward Water Gym (Required Grass Type) and then Electric Gym (Roasted your powered up Starter and Flying). My only reason for maybe doubting this choice is that the later gyms were more or less a cakewalk once your teams were sufficiently powered up.
Or you were rocking that beautiful Level 251 Misingno, none others would do the same amount of chaotic damage that taught the world the nature of IVs and how the numbers would "Roll Over" from absurdly high to non-existent due to variables we could not see or define... I miss the days of Pokemon Go where all you had was an appraisal and had to apply logic to the quotes to guess at the IV of the given Pokemon!