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I have to agree with Shaymin. None of them were that difficult...but I'll be the odd one out and say Emerald, just because of the team I had last time I beat the game.
The fact that on FR/LG you had legendaries that wouldn't of helped you as much as with kyogre or groudon. Seriously, Sapphire's elite 4 had the easiest pokemon to beat with kyogre. All you need is one electric move 2 water moves and 1 ice move.
Emerald - because I forgot about the last champion, Steve, saved the game when Rayquaza had 1/2 hp and... I had to battle when the rest of my Pokemon team fainted! I was so fumed -_- I felt so steamed up and dumb
None of them are really that hard if you bring lots of potions and revives. I can beat any pokemon league without even training beforehand. Id have to say FR/LG is the hardest though.
FR/LG because of the higher levels and the rival had a diverse team to use. Though Wallace in Emerald was better at drawing the battle out with Double Team...
Ruby was actually super hard for me, the rest were easy O_o; I don't know why. Maybe it just seemed harder because I was younger and just went head in and didn't think too much. ...Yeah, that was probably it =3 But I thought FR/LG weren't too bad once you got your Pokemon at the right levels.
When I tried out a Hoeen game, I went to the championship with 3 level 100 pokemon, so it was easy (: but... It did take me forever to get those pokemon ): I think by the time I had beaten the game I was running on 450 hours played.
I feel very contrary saying that I didn't find FR/LG elite four much of a problem. :/ I actually found the elite four for R/S/E difficult. Possibly because my pokemon were rather underleveled, so it felt like a slog when I was leveling them up in Victory Road.