Here's my guess on what could happen. While the gameplay and rosters will be the same, each game will have an emphasis on something the other doesn't. As heavily implied, the 3DS version will likely be more single player oriented with character customization and possibly where Adventure Mode ala SSE will end up. The WiiU version will be able to boast better mutliplayer options, especially in the online area. In a sense, if you want the full Smash 4 experience (assuming you care about that), you want to play both versions.
And this is some WMG, but I think because of the technology differences, Smash 4 might not go for that "realistic" look (never cared a whole lot for it), but rather something more stylized. Look at SSF4 on consoles and 3DS which is highly stylized, but the down scaling in graphics doesn't affect it too much.
Also, another suggestion. Have two different sets of character rosters. I know many may get mad on this, but I think 3DS may not have the technology to include 50 characters. I suggest the roster in the 3DS to have about 35 Nintendo-only characters (or maybe throw Sonic in there for both 3DS and Wii U) while the Wii U version have 50 characters where 5-10 of them are third party. While many popular Nintendo characters like Mario, Link, Kirby, Pikachu etc. will be available in both versions, there are characters that are exclusive on each console (e.g. Little Mac, King K. Rool, and Saki for the 3DS version while some third party characters like Megaman, Ryu, Tails, and Snake in the Wii U version).
As for the stages, it will be the same scenario like characters. Have popular stages in both the Wii U and 3DS versions while also have stages exclusive to each console.
Since there cross-compatible with each other, I suggest that any achievements unlocked, custom stages, and high scores in 3DS can be transferred to the Wii U version and vice versa. For instance, let's say you completed the Story Mode in the hardest difficult in the Wii U version and you unlocked an achievement and you don't want to unlock it again in 3DS version. With an internet connection and a special code in the save file in the 3DS version, you can transfer that said achievement to the 3DS version. This goes for the same for any high scores and custom stages you made (assuming if the later have enough space for the 3Ds version).
I also agree that KumaOso that you want play both versions if you want the full Smash 4 experience, so I suggest having
both the Wii U and 3DS versions packed into one. Much like buying two different versions of one game in a same product.