No it wont stop people from doing that, and that's not why it was created.
It's so that you can play one character with lots of different styles so that characters aren't stupidly complicated and so the designers could do lots with one character.
Also there's still a small amount of choice so if you like say sub zero but want more tools to use defensively rather than playing rush down you have that option.
I love variations and no they wont stop people picking up a new main if they don't think any variation is good enough but in any case people can stay Waaaaay more loyal to a character if they enjoy all 3 variations as they differ enough to deal with different types of characters.
Let's face it though we will want to play all of the Kast especially the new characters! So people will still have alts and be in crisis about who to play.
You can potentially play a couple variations or main just one of them but still use other characters to deal with certain matchups, it's just opening up possibilities and it opens the gate to fighting games taking an approach that is player friendly, if you're like me you'll play a character purely because you loved his or her design, so if I happened to not be able to play that character well or did not like their play style I may have picked up another character, however now I can pick someone I think is insanely cool to represent and find a variation I love on him or her, still this does not mean that there's a variation for everyone, it's likely that because the variations don't change a character entirely but only in certain ways that you may just not like character in general.