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For the gym puzzle I would say Candice's Gym. For the gym battle I would say Roark. Starting out with Chimchar wasn't good for me, going into that gym with only Chimchar, Staravia, and Shinx.
On my Platinum, the only gym that I had a problem with was Volkner, and it was probably because I was a little underleveled. Not to mention that I didn't have a ground move, and two of my Pokemon were weak to Electric. Took me three tries to defeat him, and the third try was only because I had my Empoleon left (his Raichu died of poison after killing my Togekiss. Thank god for Roserade and Toxic Spikes).
Hardest battle- Fantina, I spent too much time raising ground and normal types
Hardest gym maze- ... I dunno! Maybe Candice's snowball smashing maze?
Easiest gym battle- Candice and Maylene, I had a level 59 flareon and level 35 staraptor ready for those gyms- it was a piece of cake
As I recall in Platinum none were that hard at all due to me making my team more well rounded, but in Diamond I clearly remember always struggling on the Ghost gym, every time.
I had trouble with Wake sometimes, just because I never really have Pokemon that are very effective against his. And of course Maylene and her Lucario like to cause me pain.
I'm gonna have to say Fantina. I never really had issues with Maylene, but Fantina's stupid ghosts always gave me trouble. I just never have moves that can hit Ghosts for heavy damage at that point in the game it seems.
I've always found Gardenia tough to fight. Not so much that she's hard to beat, but with useful support moves like Reflect and Sunny Day it can become quite hard. Also taking in however fat your Pokemon can be in terms with her Roserade as well, with it's immense special attack that it comes with. D: