Look, it's not that I hate the idea of having to buy each of the games.
Here, to explain my distaste for system exclusive characters, I'll point out the inherent strengths of each system's game:
Wii U Smash Bros. = Beautiful oh my God HD, Traditional "gather 'round the TV and play,", and has less hardware limitations for going crazy with content and modes.
3DS Smash Bros. = Portable Smash Bros., the hinted at single player-focused experience, 3D effect (not a huge deal, but when implemented correctly it actually becomes a really great feature).
Now, when I think of a Smash Bros. title across two platforms, I think that there should be differences, as I've pointed out above. But what I also think is that there should be coherence between the two. That is to say, it would be disappointing to only be able to experience certain characters on the 3DS, and not be able to see them in glorious HD on the Wii U version, and vice versa with Wii U exclusive characters not being able to be used with the 3DS's unique features.
I would not be opposed to certain characters needing to be unlocked in each version by connecting your Wii U game to a copy of the 3DS one (although I can see why some would not be happy with this). I think a good solution to the 3DS storage problem is to let people load a pack (say 30 or so) of characters from the Wii U game onto the 3DS game at one time, then you can walk around with that selection of characters and make them stronger or however Sakurai is doing the customization thing. The 3DS version could have a smaller, fixed-size roster than the Wii U version, but could hold personalized data profiles for each character over the whole Smash 4 roster for a certain person (organized by Nintendo Network ID). When you copy your characters to and from the 3DS and Wii U, it takes all the data with them.
Am I making sense there? It's all very clear in my head.
But having certain characters appear only on one platform is a big no no for me.