We have done Bibbiti Bobbiti Boutique. My daughter went last June and wanted to do it again so she has an appointment during our trip this coming June. I have never seen any little girl walking around miserable, but I'm sure it has happened. With the package you are getting I wouldn't worry much about it. The ones that were uncomfortable were probably wearing the princess costumes.
It's important I think with the regular princess dresses to have something in between the dress and the child's skin for comfort. My daughter's dress was a formal gown off ebay with a satin lining, not a Disney princess dress, but she still wore a camisol and shorts under it. Her appointment was in the afternoon because we had Cinderella's Royal Table reservations for dinner, but there were two other girls we saw that morning who had already had their makeovers. One was in the Jasmine outfit, the other the Belle gown.
We saw them several times because were in the same area and ended up in the same character lines. It was raining a lot of the day but it turned out they had Royal Table reservations too and they looked just as fresh as they had that morning.
Take your photopass card for the pictures during the make over and the photo session after the makeover. We loved it and she got the left over makeup and nail polish to bring home in a cute little backpack.
I can't comment on pirate's League. My son just turned 3. I'm thinking of making an appointment for him and my nephew for next summer when we go for a big family trip. He wants to be a pirate, but I don't think he'd go for the process just yet so I'm going to wait until he's 4.