Overall it's hard to say, because it will vary by MU. Marie struggles more against characters with exceptional spacing control, whereas Nyo has a superior range game. But, Marie has the better CQ pressure.
Phase 4 is undoubtedly the worst, though.
Also, Nyo is a fine character. I mean, she's no Leifang or Genfu, but she's got a good bag of tricks for those who are dedicated enough to brave the learning curve (which is not very many).
Well I think we all know P4 is the worst out of the three. Nyo has some very good spacing and incredible damage output. Haven't played with Marie so I'm pretty biased on her.
Phase 4 is undoubtedly the worst, though.