It might surprise you to learn that the Portal 2 Steam Workshop is the busiest of all Workshop's mod repositories. There are over 302,000 items on there, so I had to narrow the search down somewhat. I chose innovation as my main filter. I've been on the lookout for game-changing mods: the new challenges that haven't been seen before, creative level-design that Valve forgot, and additions to the base game that creates new ways of solving puzzles. Here are the best I found.
First up, Quantum Entanglement. There are some obvious additions that that you could add to Portal 2: a wall-climbing gel, a third-Portal, or a pair of magic shoes perhaps? But this is totally out of left-field: in Quantum Entanglement the puzzles take place in rooms where you can move one cube and another cube will mimic that movement. It's a bit like a single-player co-op game, where you move your cube around, using all the usual Portal 2 tools, and the other will activate switches. It's by turns baffling then enlightingly brilliant.
Link: Quantum Entanglement