She definitely has weakness. I've played like 250+ Vi games in the past 6-8 weeks, I just started playing Vi because she's cool and I wanted to learn my next champ. Nid, Fizz, and Xin are really good vs Vi, Nunu is decent because he can kite Vi all day. Peel destroys Vi, having a Braum, Thresh, or Morg support is very good vs Vi. Highly mobile marksmans work great vs Vi, such as Kalista and Lucian. Vayne is also a good mobile marksman, and probably the best marksman vs Vi since Vi usually stacks HP and Vayne will shred Vi. Mids like Zed, Azir, Cass, Ahri, Karthus, and Orianna are great vs Vi. Good top laners would probably be Singed, Jax, Jayce, and Gnar.
She barely has any mobility, why take it away? Her only mobility is her Q, which has to charge and reduces her speed while charging. Her early and mid game is being nerfed in the next patch. Her lvl 1 ult damage was reduced by 50, and her lvl 2 ult was reduced by 25, but lvl 3 does normal damage. She has plenty of counter play, you just have to play her 250+ times to learn what she's bad against.