Twilight Princess was definitely harder than the Wind Waker, in my opinion. One of the main factors to why it was harder for me was that Twilight Princess was my first Zelda game. So that meant I had to learn how to do everything and when I first started I got scared to fight a simple Keese.
I think Twilight Princess had harder puzzles than the Wind Waker. The Wind Waker's puzzles felt like no-brainers to me and I didn't get stuck at all on the game. Twilight Princess had me stuck on puzzles for a good half hour maybe, especially when it comes to pushing blocks on ice.
As for the bosses, I still think Twilight Princess was harder. Morpheel gave me a lot of trouble when I fought him and I was clueless as how to fight Zant when that time came. The only boss in the Wind Waker that I found hard was Puppet Ganon in Snake form, and that really wasn't hard, but annoying.
When it comes to completing the game 100%, the Wind Waker is definitely harder. Twilight Princess's side quest were all too easy. The Golden Bug was simple; whereever you found one gender of the bug, the other gender is somewhere else in that area. The Pieces of Heart can be located with the fortune teller in Castle Town. The only hard one in Twilight Princess is the Poe's Souls. The Wind Waker had some side quests that really weren't hard, but tedious. The Goron Merchant one, for example, had you going to those three different islands and bringing new items and losing rupees, all for a Piece of Heart. Even getting all 20 heart containers was challenging, which I never actually did.
Overall, Twilight Princess was a harder game.