If we're going by gameplay we've already seen, the 3DS grand finals were far superior to the Wii U tournament we saw at E3. The players that made it much farther in clearly knew more about how the game works than anyone at the Wii U invitational.
That said, some of the most hype matches I've seen were the personal "grudge matches" on the Wii U during SDCC, featuring characters like Rosalina, Samus, and Zelda showing intelligent tactics and hidden potential alongside more obvious choices like Fox and Bowser.
As for which one will be more exciting to watch in the future? That depends on the style of play or even the individual tournament. The Wii U version is visually impressive and you can see the percent meters on the same screen. The 3DS version, on the other hand, has good stages with some pretty interesting stage hazards and gimmicks that would be cool to see put to use in a competitive fashion (only up and down blast lines on Balloon Fight, and you or your opponent can always attack or approach from the left or right regardless of your position on the stage), though some of them are gonna be illegal for fairly obvious reasons. (Hello, Golden Plains.)