It's not so much an idea I picked up from anything. It just seems obvious to me, so admittedly opinion. It's a full game in of itself, true. However the Wii U version is a bigger beast in a sense and is most certainly the "main" version as far as content is concerned. I'm not saying this to say the 3DS version is garbage or bad or anything. Just that ever since both versions were announced, and announced to be coming out close to each other, I've always felt that the Wii U version would be the main one. They want to help push Wii Us after all, and no longer need to "save" the 3DS.
Hardcore Smash fans will buy both most likely. If the Wii U has no extra characters and just more modes/music, the average Joe may look at both and just go "Well I've got it for my 3DS. I don't need to buy a Wii U now just for this if the characters are all the same." Which is not what they want, they want people to get interested in the Wii U version. Heck there may not even be extra characters for the Wii U version initially. If not I'm just not so sure any amount of modes or marketing can really sway people to snag it for the Wii U or a Wii U in general. Me being one of them and I even own a Wii U.
Back to IC real quick as I know I keep touching on them, even though I don't play them ever. I don't think them being exclusive to the Wii U version due to 3DS limitations would be bad. It may make some 3DS users upset, but they're not in the 3DS version anyway. Wouldn't it be petty for them to demand that the Wii U owners aren't allowed to have them either? They're the only major constant veteran with a unique move set that has been cut. Doesn't seem fair. Then again as I said I'm pulling for Mewtwo to come back as well so the Wii U version is really the last hope some people have. Perhaps the IC could be added later and only accessible to the New 3DS? Not fair exactly but it's an option, and Nintendo has had content in games for newer hardware revisions before like Links Awakening, DSi download store, etc.