The only real reason to get the 3DS version is if:
- You really want to play the Wind Waker epilogue
- You really want to play the Linkle story
- You really want to play the Wind Waker Adventure Maps (or any of the adventure maps from the second season pass)
The Wind Waker and Linkle stories are good, but not worth the significant downgrade in presentation. I'm not usually a guy who harps on or cares about graphics, but the game seriously loses something when compared to the Wii U version.
The adventure maps... losing those can hurt, if you're into them. I'm STILL playing that game largely because the adventure maps, and not having the WW, Link's Awakening, or ALBW adventure maps on Wii U hurts. That said, there's already tons of content in the Wii U version, particularly with all the DLC, so not having those three maps may not matter to you.
The only other real downside of the Wii U version is that to get all the content you can, you need to buy two season passes and the Legends pass that gets you all the characters from the 3DS version + Gannondorf's trident weapon. That's a noticeable cost sink, considering everything from the first season pass and the Legends pack is included in the 3DS version (buying the 3DS version also gets you a code for the Legends pack for free in the Wii U version).
The base game comes packed with content as is on the Wii U though, and the two season passes + Legends pack are more than worth it. If that's not a huge detriment to you, I'd stick to the Wii U version. Everything beyond the points mentioned above is largely inconsequential - character switching can be nice but isn't essential (and honestly I almost never used it), and the Fairy stuff is pretty much completely worthless.