Honestly, my inherent need for instant gratification would probably influence me to buy the 3DS version. However, at that point, I would probably want the Wii U version as that is quite clearly the superior version with all of the longevity. Controls are subjective, but it is going to be easier to use your controller of preference than the 3DS despite the notion that others found the controls "easy to get used to." Basically, that means, "it is possible and not as bad as you thought it was going to be." I have not heard ANYONE assert that they preferred the 3DS controls.
As others have mentioned, if there are other games in the 3DS library that you are interested in... it is worth the investment. However, if you are not interested in: Kid Icarus Uprising, Fire Emblem Awakening, Pokemon X and Y, Mario Kart 7, Luigi's Mansion Dark Moon, Super Mario 3D Land, Bravely Default, Professor Layton and/or Ace Attorney, Kirby Triple Deluxe, Animal Crossing New Leaf, Legend of Zelda A Link Between Worlds, or the 3DS remakes of Nintendo 64 classics: Star Fox 64 or Ocarina of Time... it is not worth the investment.
I tried to list out the 3DS titles worth a damn. If you only had to get one, I would base your decision off of other games, rather than Smash as anyone who is competent understands that the Wii U version is better for Smash. The only detriment is that it is not portable. So I suppose if that is relevant to your needs, consider that. For instance, I do not care about portability. I play my 3DS exclusively at home. So that point is moot regarding my habits. If you are interested in two or three titles that I listed above, it is probably worth the investment of a 2DS at the very least.