Some of them are too big and tbh just wouldn't look good on 3DS
That kind of answers part of your original question. My full answer:
1. If that were the case, then Smash 3DS would be
strictly inferior. While many already believe Smash Wii U is the better game (and many who bought the 3DS version did so only because of its earlier release date), Sakurai intended for them to be equally enjoyable as standalone games.
2. (The point you touched on) The 3DS stages are in lower resolution/quality. It takes time and resources to make the stages that look just fine on 3DS even remotely acceptable on Wii U.
3. Tying into #1, basically the only reason to buy the 3DS other than its earlier launch date (portability and Smash Run might also be factors, but they're smaller ones) is the stages. You'd basically be making the 3DS a not-even-free demo for the Wii U version.