I wasn't all that keen on Vanessa either, at the start of the film I found her incredibly annoying, such a perfectionist and so serious all of the time (although she has perfectly good reason to be both of those things given her current situation.)
However as the film goes on my attitude to Mark and Vanessa flips, I liked Mark up until he decided to leave his wife (and also gets a tad weird with Juno) and Vanessa really grows on you. That particular scene where Juno has just found out that Mark is leaving, and has come downstairs crying only to come face to face with Vanessa. She tries to hide her tears, and Mark tries to lie but Vanessa immediately knows its something Mark did, 'what did you do?' Thats when I started to like Vanessa, and I think she was genuinely lovely person, it was just hard to see because of some of he bad things that have happened to her.
The funny thing is that Juno herself probably thought similar to the way we did, she instantly thought Mark was really cool, she liked the fact he liked the same music/movies as her, and she sort of just forgot about Vanessa. Her mind changed, like mine did, when she saw which one of them truly cared about her and her baby
Although M and V were DEFINITELY not suited as a couple, they couldn't have been any more different.