Most likely yes.

They could have released the Wii U one first then announce a 3DS version a few months after launch, That way any Wii U hardware boosts would have died off by then.

they can delay it.
Let wii U version be the only version avaliable at holidays, and launch 3DS version in feburary.

They could also make some crude decisions, like: you only open a character if you have/play with the wii U version. make the wii U version complete the 3DS's.

I think so. I think they were counting on the huge success of 3DS to make the game and WiiU more appealing, showing that their will be alot of interaction between the two consoles. But the connections between 3DS and WiiU are non existent, the WiiU is bombing and instead of making the WiiU more appealing, the 3DS version is making the WiiU less essential for some.

At this point it's looking like the Wii U is a lost cause so for them the 3DS version may be a way to squeeze out more profits from the game.

Certainly, 3DS doesnt need SSB, it's useless on 3DS in sales term, it would have been better as a Wii U exclusive.

They should have at least change the characters between the 2 versions, not only some stages

I doubt that it affects their bottom line negatively, and I doubt that they care about the 'console wars'.

I doubt that they regret it.

I don't think they have regrets. Why?

On 3DS, yes, it's the best-selling handheld on this generation but talking about 2013 sales? It's actually slowing down.

And lastly, both Wii U and 3DS has some difference. Just watch TheJWittz's videos ;)