Curl, I had this initial reaction too. I think Nintendo is wise to keep its products seperate so they don't fight each other. However, the more I thought about it and the more I learned about the SSB4 project, the more I realised it is a good idea to have it on both, because:
-they will not be the same game.
-after a huge 2013, 3DS is going to need a big title for 2014.
-the 3DS title will likely be a complementary title to the WiiU flagship.
-the Wii U experience will be much bigger and better.
-the large audience playing on 3DS will lead people to buying the Wii U and its version.
It's this last point that is relevant. Nintendo really needs to use 3DS as a gateway drug. Many, many gamers have their first experiences on a Nintendo handheld. If all of them moved on to or added Nintendo home consoles, Nintendo would dominate the market. I think a 3DS game that encourages consumers to pick up the Wii U version could be huge. It could also make the Wii U Smash really seem like a next-gen title after playing the inferior 3DS title. I think we saw a little bit of this potential with people loving NSMB and then picking up NSMBWii and it's 4-player chaos. More efforts like this could only help Nintendo's position.