I have both, and I rather play home consoles than handhelds.
3DS had (still has) a brilliant life. Many games are great, and had a great Japanese third party support. One of my favorite games of the generations, Shin Megami Tensei IV, is for this console (I will tell you if Apocalypse is better when I finish it). Its main bet was the 3D screen without glasses, that was a little shitty in regular 3DS, but well improved in New 3DS; unfortunately, doesn't seem to be a relevant factor of the handheld, nobody cares much about it, all people think about the games.
Meanwhile, Wii U,... Well, we all know it had no third party support (had, but not much), not many games. Many games were great, others weren't, and some had a bad reception because we need to play with the gamepad. Not everyone liked the gamepad, I personally hate it, but we had the glorious Pro-Controller, a great controller with an insane battery life. I enjoyed, and still enjoy, the console. I'm also a PS4 owner, and play more often with my Wii U than with my PS4, and this one is supposed to have a huge library. Overall, I'm happy.
I think both did well. The Wii U had many failures, but I'm proud of having it.
Let's see how NX performs, and if they have learned the lessons after the Wii U.