I think everyone's reading a little too much into the fact that she never ever was supposed to be integrated into the Muppets proper.
If you can get through the titanic brainfart that is Agent K leaving the Men in Black with his memory wiped, only to randomly pop back up in the cartoon series... and it isn't even supposed to be interlinked with the second movie, since J forced L out of the MIB in between films... oh, and now she's blonde.... not to mention no references towards Agent Alpha in MIB 2 or 3 (though it would have been far superior for either film to have him as the main plot...especially that second one).
Essentially, the animated version of something is never taken into canon... even acknowledged by the live action team. It took a massive internet campaign for them to retcon the animated Star Trek episodes as canonical to the TV series.
I just find it sorta hilarious that this thread has stayed consistently at the top since two years after I joined like it's a grand question, and the second post pretty much answers it.
I think even though it was a spin-off a lot of people grew up with it from the 80s-90s and many even saw that first (which is why the baby versions are often referenced alone), so people got confused when Skeeter didn't turn out to be one of the family. Even though the real answer was "they wanted another girl so they made one up for some reason." I guess it'd be like all the people that grew up with
DuckTales wondering why Launchpad isn't in the Scrooge comics. The answer is simple but they're so familiar "that can't be it." Or maybe people just really love Howie Mandel? I can't see Skeeter contributing much other than "HEYSHE'SFROMTHECARTOON", though anything's possible if written well. I really find it odd that so many people still ask when even in
Takes Manhattan they say it's all imaginary--Oh, but there was that thing in
Family Christmas so...hm. Yeah, it's still odd.
....I can kinda see Karen Prell rocking a puppet version of her though.