I always loved Mulan not because I thought she wanted to be a man but because when I was little she showed me just how awesome women could be because she went into the army and while she might have worn men's clothing and "pretended" there was no pretending how awesome she was. I don't think she ever identified as being male, at least not in the movie, but that was always ok with me

Her cross-dressing was a means to an end to protect her family and her country, but she was awesome when she was in girl-mode and also when people thought she was a guy.
But if you didn't like those certain parts I wouldn't recommend watching the sequel to the first Mulan movie.
Some of my favorite disney moves are The Fox and the Hound, Mulan, The Lion King, Oliver and Company, Robin Hood and Lilo & Stitch.