Hmm my opinion.
I miss smash run, I wish they put both modes just for the sake of it. I relied on run for custom move grinding.
Fortunately, I unlocked everything on 3DS, and I've played enough times to get top notch equipment, stats, etc, and I can transfer it to the Wii U. Drawbacks are you can't edit custom characters that are transferred and you have take some considerable time to transfer customs every. darn. time. you want to update it.
I see the opposite on stages. I'm not tired of anything yet. The HUGE plus on the Wii U stages is that 1/8 of them such as Great Cave Offensive ruin the fun, while the remainder are what I think are fair. However, on 3DS, 1/2 of them are fair only. Therefore, For Fun on Wii U is better. On Wii U, I can run into Halberd, Skyloft, and about 5 more good stages before running into something like Flat Zone X. However, on 3DS, chances are the only stages on For Fun are stupid ones, such as Brinstar, Flat Zone 2, Green Hill Zone, and Mushroomy Kingdom.
And an obvious drawback to Wii U is that chances are your friends don't even have a Wii U, and the only way to play is for them to come over to your home. The 3DS mostly solves this.