Since that show was on the air for 8 seasons, and another decade after that in syndication, one would think that Skeeter's popularity would guarantee her a spot in a real Muppet movie.
I think the number of people aware of the Muppet Show (1976) and the older Muppet Movies foreshadow those that know about Muppet Babies (1984). Since in Muppet Babies most of the characters were the babies (except for the occasional parent figure), the gender roles were unbalanced. Thus the addition of Skeeter.
Though this is not to say that this is the reason why Skeeter was left out. There were other Muppet movies before "the Muppets" where Skeeter was not previously included.
- The Muppet Movie (Uncle Deadly, Scooter)
- Muppets from Space (Uncle Deadly, Scooter)
- The Muppets Go Hollywood
- Muppet Treasure Island (Uncle Deadly, Scooter)
- The Muppets Take Manhattan (Uncle Deadly, Scooter)
- The Muppets' Wizard of Oz (Scooter)
I could be missing some, the full listing including 1 hour long tv specials could be found on the Muppets Wiki page.
I am just going with why Skeeter was included in the Muppet Babies but not the other way. So you will have to ask why Skeeter was not included in any movies from 1984 onwards.
In response to the rights, I think it is logical to believe that Disney owns the rights to all characters. Not taking up rights just for Skeeter does not make any sense.
I decided to do some digging on the forums, and I stumbled on to a thread that asked Muppet writer Jim Lewis about placing Skeeter into family in 2008,
No. Why? Not really sure, to be honest. It could work, but I still see
her as a Muppet Baby, a balance for Scooter (His Bookishness to her
tom boy-ishness). I guess if she could be developed into something
more, a force in her own right as an adult, it might work. But I'm not
convinced. Plus, I'm lazy which is why I'm going to stop thinking on
this too much before my head starts to hurt.
Also in a separate Ask Jim session
Ahh, Skeeter. I wasn't there for the creation of the "Muppet Babies"
animated series, but I suspect she was added to the show so there'd be
another (dare I say, more balanced than Baby Piggy) female character
on a show aimed at kids. We threw around various bizarre scenarios
about what happened to Skeeter after "Muppet Babies," but none of
these were ever confirmed. Frankly, I suggest contacting the Federal
Witness Protection Program for more info. Let us know what you find