‘Team Misato’ refers to the team that believes Shinji is best suited to Misato. This is in contrast to teams Asuka and Rei.
Now, let’s be clear: this ain’t ever happenin’. Them’s the facts.
However, that doesn’t mean Misato isn’t best girl because, obviously, she is.
The thing is that Misato is more like an older sister or weird mom to Shinji, rather than a romantic interest…well, despite that whole kiss thing; let’s not worry about it.
I don’t think there are any continuities where Misato wins.