ZSS's moveset is not based on the whip either, her moveset is based around kicks more than anything. Only four moves actually used the whip besides her grapple (Up B, Side B, Side Smash, Up Smash). Heck, in Smash 4, her Up B no longer uses the whip, it's now a jet powered kick. Her whip was also a gun.
As for why the used a whip over something like a Beam Sword, we already have a beam sword as an item, plus we have plenty of sword wielding characters, so it would make her more generic. A whip is not something we have seen much of in Smash. Plus, Samus uses a grapple in her Power Suit that is also a whip, so whips are an established part of her arsenal.
They gave Samus jet powered heels because they add more power to her kick based moveset (kicks from heels hurt like hell), and the heels themselves serve as a funnel for the rocket. I don't even know how jet gloves could possibly work.
Samus had a beauty mark in Other M, and the Smash 4 design is based off of Other M. So that's why she has it in Smash. For anyone to care about a beauty mark is really reaching for straws here, anyway. It's literally just a spot of black on her face. And it's barely visible (I can't even see it in the render I posted, but it is in screenshots).
The picture with the bunny ears is just a silly little joke on Sakurai's part and does not say anything about how the character herself actually is in the game. Such is the beauty of camera mode in Smash. This is not the first picture like this we have gotten. Take this for example:
The sexual innuendo is blatant. She looks like she's orgasming. Yet nothing about her portrayal is sexualised. It's just Sakurai making fun of the characters.