I wouldn't count the first run an offical elite 4 challenge since Ghetsis had nothing to do with the elite 4 in the first place and even though N was considered the champion after beating alder,it wasn't like you could face him a 2nd or 3rd time just like how you could face alder as many times as you want once you beat the game since he's considered the real champion.
for me the hardest pokemon league was either johto or hoenn. kanto league wasnt too hard if you reach a certain lvl, the only challenge in the sinnoh league was the champion, and the unova league was the easiest.
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