Even though I am still enjoying both my 3DS and Wii U, I'll give my thoughts on them up to this point.
The 3DS is my favourite handheld of all-time. The library is fantastic. Games like Fire Emblem Awakening and Fates, Super Mario 3D Land, A Link Between Worlds, Animal Crossing New Leaf, Luigi's Mansion Dark Moon... I mean, yikes! I love these games and more (3D versions of OoT and MM come to mind). Also, I really love the StreetPass function. I hope Nintendo will continue to implement that feature. My 3DS joined me on the road while I backpacked, so it will always be special to me for that reason alone.
The Wii U was the first Nintendo console that I did not buy at launch. I finally picked one up a year later (after a two-year break from video games) and I was immediately reminded why I enjoyed Nintendo's products. It's not perfect, there's no doubt, but there are a lot of fun games and that's what I want. I'll always fondly remember SM3DW, Mario Kart 8, Super Mario Maker, Xenoblade Chronicles X, Hyrule Warriors, Splatoon, The Wonderful 101, Pikmin 3, and Tokyo Mirage Sessions #FE, among others. (Captain Toad, DKCTF, the HD Zeldas... man, top-notch stuff.)
The Wii U severely lacked third-party games, but it is where I first played a Splinter Cell game (loved Blacklist!) and it's also where I first played Deus Ex: Human Revolution (absolutely incredible game). And to this day, ZombiU remains one of my favourite games on the console.
Also, Off-TV play is amazing. It's been perfect for me to be able to play games while my girlfriend watches her shows. It's something about the Wii U that I didn't know I wanted, but couldn't have been better for my situation.
So, I guess to sum up, I'll remember that neither were perfect, but both had great games that I loved to play.