If SSB3DS came out at the same time as SSBWU, I think it would be crushed. "Why play this one when I can play this cooler lookin one?" Surely it'd sell to those with a 3DS but not a Wii U, and people who prefer handheld gaming, and us goobers who plan to buy both no matter what, but at the very least there'd be serious competition for attention within the marketplace, and competition for attention from those gamers who buy both versions. I know I'd be torn between the two versions if I got them together, why play 3DS when I can off-screen the Wii U one? (This ignores the obvious huge difference in ownership rates between the 3DS and Wii U.)
If SSB3DS came out AFTER SSBWU, we'd have the issue of it having to "one-up" the Wii U version. Everyone and their mother would've already played it one way or another on the Wii U since a console followup to this traditionally console-based series is going to get the most attention, a new version would probably go pretty overlooked when even if it brought some new stuff to the table, it was inherently smaller in its portableness and tininess and not-as-good-looking-ness. I'd see a ton of people just sticking with the one they already have.
With SSB3DS coming out BEFORE SSBWU, I think we have the optimal situation. It plays out the same as the 3DS-after-WU scenario, but I think the difference is that the Wii U edition CAN successfully one-up the 3DS one. The 3DS's characteristics prop it up as a first course, an entry to the world of SSB4, and the main course finally arrives in the winter, with everyone primed and ready for the big fat graphics, stages, and new modes. Friends all congregate as they should, after an extended 6-month 3DS beta. Conceivably the hype could be HIGHER than if the 3DS version never existed at all.