Well, I have many games for both in my backlog so I'm not the most informed, but in my limited time with both, I'd say 3ds just by a hair. Both are two of my favorite consoles ever.
3DS - Luigi's Mansion: DM, Zelda: ALBW, Resident Evil: Revelations, Pokemon: OR/AS; X/Y, Monster Hunter 4U, Ocarina of Time 3d, SMT IV, and Bravely Default. I haven't even gotten to Majora's Mask 3D, Code Name: Steam, Fire Emblem or Animal Crossing yet, not to mention Kid Icarus, Kingdom Hearts: DDD, Starfox 64 3D, etc. So much variety and incredible experiences.
Wii U - Mario Kart 8, Smash Bros, Bayonetta 2 (and 1), DK: TF, Hyrule Warriors, ZombiU, Wonderful 101, Splatoon, and Super Mario 3D World. Still on my backlog: Windwaker HD, Captain Toad, Kirby, and Pikmin 3. Lots and lots of fun with amazing games, but not quite to the level of 3ds.
I think my experience on 3DS has been more well-rounded, but it's so close. Almost too tough to decide. I'd say 55% in favor of 3ds, 45% Wii U.
Upcoming titles, I'm way more excited for Wii U than 3DS, though.
It'll be awhile before I figure out how to do one of these. :P
