I think the general sentiment is that once the Wii U version is out, the 3DS version will see a lot less playtime for most people. This gives the 3DS version roughly a month or so of playtime while most people will have much, much longer legs. This is some generalizing, of course, since I personally plan to play the 3DS version a lot while I'm on-campus and the Wii U version whenever I'm home. That said, if I could describe a perfect situation for myself, it would be that all of the time and resources that went into the 3DS version went into creating a Wii U version that is bigger than the one we're going to get (even though I'm positive these games will both be enormous in their own rights). So, I'm not sure that anyone hates the 3DS version, but I do think a lot of people wish it weren't being made. I wish Smash Run were in the Wii U version instead. I wish all of the fun, quirky looking stages like the Spirit Train were on the Wii U version instead. I wish all the trophies from the 3DS version were in the Wii U version instead. It's just a matter of preference. I am sure the 3DS version will be excellent (I even played it at Best Buy and liked it a lot), but I play Smash with my friends on my couch while kicking back a few drinks, and if those are the circumstances, I'm playing the Wii U version.
It's sort of like the Subspace Emissary in Brawl. So much time and effort was put into that mode for something that ended up being sort of boring once the novelty wore off. It wasn't replayable, and it's hard to even find it fun anymore, personally. Perhaps the time and resources that went into SSE could have given us a few extra characters, stages, songs, etc. Obviously I don't know how the game was developed, and I doubt the same group of people who made the videos, stages, and assets for SSE were also creating stages and characters. But if they had knowledge of how to make those things then surely they could have helped to make some extras that people would appreciate years from then. I don't think Smash 3DS will end up being boring, but I do think the Wii U version could potentially overshadow it, and if it does there are going to be a lot of people wishing that the time put into the weaker version was put into one singular and meatier experience instead.