I haven't seen TMTM for a long time but I do remember from the comic book adaptation Piggy saying to Kermit that she wishes that they could have met much sooner. And Kermit replies like when they were little kids.
This then leads into the Muppet Babies sequence and in its context does imply that it is just a fantasy in Piggy's imagination. However the Muppets have never been sticklers for strict continuity. At least the possibility is there to just introduce an adult Skeeter Muppet to a new movie or television series as Scooter's twin sister and they don't even need to make reference to Muppet Babies or any other origin. Just like many characters throughout The Muppet Show and Muppets Tonight usually just made appearances often with little or no background explanations and some also disappeared with no explanation.
I like Skeetere because she is such a contrasting character to Miss Piggy. I can't speak for anyone else, but I think that there needs to be another strong female character besides Miss Piggy and Janice (Yes, I included Janice).