I think they became a big part in later seasons.  I know there were in at least one vesion of the openeing.  But they would always visit.  They didn't live with the other muppet babies.  I suppose it wouldn't make sense to jst have them live there all of a sudden.
I'd like to see an adult Skeeter in puppet form as a special guest puppet on a new show.  Maybe not a full time character (though that wouldn't be bad if done right).  It could be interesting, though hard core fans would be so mad.  However, i think it would be good as long as they don't mention the muppet babies.  If she was introduced as a new character that no one but Scooter knows about it would be cool.  It would be a name that people would know, but a blank slate as well.