In this thread, imagine that Game Freak came up to you and said "hey, we want to put your idea in the next Pokemon game." Tell the world what you would do with that privilege.
For example, if I got to design a gym, I'd make myself the leader of a Ground type gym in a grid based game. The field gimmick would be that all my trainers have their sight following you no matter whether you walk or run, and it's in an open field so you can't dodge around them unless you use the gimmick, which is kicking sand off the ground into their faces, blinding them temporarily so you can pass by without fighting. You can do this after you beat the trainers as well. The more trainers you kick sand at, the stronger my team will be at the end of the gym, level-wise. It would likely be an early gym, so I'd probably just have a Sandshrew and a Sandslash.
I've got longer (wall of text) descriptions of what I'd do if I led an evil team or the Elite Four, but I'll spare you for the very first post in this thread. Be as verbose and descriptive as you want. You could make an entirely new Pokemon, or design an entire storyline around your evil team, if you want. I did the second one, personally. Get creative!
I admit that this is less a game and more a creative exercise, but I feel like it wouldn't fit in GD.