It often feels like she's outside the main story, but in an interesting way. She has off-handed comments about the choices characters are making. Although she doesn't directly break the fourth wall I feel myself relating to her because of these asides.
Her motivations aren't as complicated as the other characters, and it makes her easy to like. She doesn't have angst or conflicting memories and emotions. She wants Materia and she'll do whatever she needs to do to get it. Maybe I just like her because I'm also on the hunt for Materia and I want to collect it all! She's also the closest thing to a ninja in the FFVII universe, so that's cool.
On the other hand, Vincent is a little too serious for me. He's very brooding and doesn't have a lighthearted bone in his body. His story is more directly related to the main story than Yuffie's is, so he definitely has to be more serious. I just didn't find him as enjoyable to have in my main party. He gets to wait on the sidelines.
There are a few times that specific characters need to be in the party for quests. Whenever that isn't the case my main party is now Cloud, Tifa, and Yuffie. I'm probably going to keep it that way until the end of the game.
I'm now sitting at 20 hours of play time and I'm on disc 2 out of 3.