I own both version and actually hate how there are so many stages that could be on both that aren't. For me, being able to play Smash Bros on the go is more than enough reason to get the 3DS version and being able to play it on one system with friends reason for the Wii U. Splitting up fun levels is unnecessary.
3DS to Wii
Top Picks
Brinstar - Tons of fun in Melee, it's the least chaotic Metroid stage currently in Smash Bros 4. It'd be great to see in HD
Wario Ware - A shame this one is stuck on the 3DS only, it works better on the version that focuses more on/is easier to do multiplayer
Gerudo Valley - A fun and fair stage, it'd be big enough to support 8 Player mode too
Green Hill Zone - The better Sonic stage, it could probably work with 8 Player mode too
Mute City - Good to have a new F-Zero stage on the Wii U, also provides something different from the travel/land formula that is overdone in the Wii U version
Second Picks
Pictochat - Another fun and unpredictable stage that would be better for the version that has more multiplayer options
Corneria - Another classic that is still fun to play on
Living Room - Another 8 Player candidate, the changing layout is fun to play on and the Puppies would be cute in HD
Yoshi's Island (B) - A fun, competitively viable stage
Tortimer Island - Fun layout and would make use of the swimming mechanic
Bonus Picks
Magicant - Very nice visually, the Flying Man hazard is unique and would be fun to have
Mushroomy Kingdom - It was a fun auto-scrolling stage
Distant Planet - A fun stage, though hard to see, it was fun to try and get opponents eaten
Kongo Jungle - Another one that is harder to see in, but one of the better DK stage, also 8 Player potential
Prism Tower - A fair stage that doesn't really interfere with the battle too much
Pac Maze - Another fun stage but I wonder if the Power Pellet gimmick will work with all players sharing the same screen
Arena Ferox - The changing layout makes it fun and it just is better designed than Colosseum
Super Mario 3D Land - Another fun Autoscrolling Level
Tomodachi Life - Another 8 Player candidate, plus I love seeing the random Miis in the background
Wii U to 3DS
Top Picks
Onett - Still the best Mother stage, it has a fun layout and looks cool, the cars are fun to deal with too
Castle Siege - The changing field has always been fun and they layouts are good too
Halberd - The hazards really make this one
Gamer - Trying to avoid Mom made this stage pretty fun
Mario Circuit (B) - The Shy Guys were fun to avoid and I like how it didn't travel the course
Custom Stage - It'd be amazing to be able to download and play on Custom Stages on the 3DS, even if they cannot be made in that version
Second Picks
Kongo Jungle 64 - A neutral layout, the cannon makes for fun recoveries
Lylat Cruise - Another pretty fair stage with little hazards to ruin the fun of battle
Yoshi's Island (M) - A good, small stage that always lead to some wild battles
Delfino Plaza - A fun stage with changing layouts, it'd be interesting to see how it works without swimming
Bridge of Eldin - While flat, the destructible middle and the "horseback" foe made a good hazard
Bonus Picks
Luigi's Mansion - A simple stage that lead to some chaotic matches with the whole destructible layout
Skyloft - Another fun traveling stage
Pirate Ship - While losing swimming takes away my favorite part of it, the other hazards were still fun to play with
Pilot Wings - An interesting and predictable stage, the 3DS should be able to handle this
Wii Fit Studio - Wii Fit Trainer is the only character that isn't R.O.B. that lacks a home on the 3DS now, remove the mirror and it should work fine
Sky World - The best Kid Icarus stage, it's pretty fun to play on
Pac Land - I actually enjoyed this stage, it'd be nice to have another autoscroller
Smashville - Another fair stage that doesn't disrupt battle
Norfair - If the 3DS can handle it, it's a very fun stage
Windy Hill - Not as fun as Green Hills but still a good stage
I'm not rich, but I would pay for all of these (over time) and any other Past Stage as well
