Oh, that's a tough one. Platinum was actually my first Pokemon game!
I think for me Gardenia was always the most tough, even though she was only the second gym leader. Now, whether she was actually tough to beat or whether I just didn't train enough before challenging her I'm not so sure, but I highly assume it's the latter. Not to mention I chose Piplup as my starter the first 3 or 4 times of going through the game, so she almost always had the advantage unless I got my hands on a fire type beforehand.
My least favorite gym layout, however, would be the freaking Maylene's fighting type gym. I ALWAYS dread reaching that point in the game...T-T
My favorite would probably be Fantina, because ghosts, her gym has a super cool strategy and layout, and I mean, who doesn't love Pokemon Contests? ^-^