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Hmm... In the original Gold/Silver, I thought all the gyms were rather tough except for Price. That guy was so easy. In each of my run throughs and versions I had problems with each gym leader somewhere along the line. Heart Gold/Soul Silver just made all the gyms really easy for some reason.
That Gengar (forgot the gym leader name) made my life very very very very very hard. I can handle the milk tank, but that ghost just killed my pokemon by just looking at them.
In my opinion, Morty. Some people say they powned him easily. But I had a hard time facing his Gengar. Woot. That Gengar packs a punch. Whitney was pretty hard, but she took only 3 mins of my time to beat her.
It's usually between Whitney and Clair, I find. In GSC, Whitney was VERY difficult to beat because of her Miltank, but in HGSS something about her just seemed so much more managable. Clair on the other hand was harder than ever to beat; in each playthrough of HeartGold I find that I only ever beat her with the skin of my teeth, and I never had anything that could handle Kingdra too well- I the last time I fought her I basically had to wait til it could only use Hyper Beam. :/
Whitney was a struggle for me until I remembered the almighty power of Heracross. Level that thing up 17 and you're rolling through that gym like a piece of cake.
That Miltank was the most challenging pokemon to beat in the entire game for me.
But when I finally took it down, was the best IN YOUR FLYING FLIPPING FACE moment.
I always had trouble with Bugsy's Scyther and Whitney's Miltank. Especially in GSC, that Scyther was awful. I think on my first playthrough of Gold, it took me at least 5 challenges to beat Bugsy just because of Scyther. And everyone knows that Whitney's Miltank doesn't take names. My most recent runthrough of HeartGold was the first time I didn't have to make multiple challenges against Whitney (got lucky with a burn from Quilava).
I had problems with chuck; I was underleveled when I got there :( had to grind oh so long.... whitney as well, every time I think I got her, she uses the stupid recovery move! I took forever with her... and after that I seriously though I won't get the badge cuz she was a sore loser xD
I actually think Whitney is easier in HGSS than in GSC but still remains tough, Clair on the other hand is slightly more difficult so it's really a tie between them.
Though not as difficult for me as most, I would have to say Whitney was the most difficult to face in terms of relativity. (Miltank was only mildly annoying.) Claire took me the longest and had the highest levels.