Ah - the eternal question: "How does one count the Muppets". I congratulate anyone who even attempts such a thing not only due to the large number but by the fact that to even do such a thing, you have to set a large number of parameters which are logistical nightmares, one of them being discussed here is what productions/families/casts do you include and leave out. Not simple since there are so many of those "exceptions" and grey areas. Take Skeeter (since she was recently mentioned) - she's not been made in Muppet form but she has been made in "Poser Muppet" form.
Muppets are continually recycled into different characters - Mopatop's being a good example - do you count those once or twice. Even when a puppet isn't really rebuilt but has a totally different identity, does it get counted once or twice (example: Cookie Monster vs. Arnold) You can decide to leave out Wubbulous World but then you have puppets used in that show that made crossovers into other productions.
And then there's the Whatnots/Anything Muppets - do you include everytime a new Muppet is made up from an AM even if it's just as a one-time background extra?
Good luck to anyone who ventures down such a path!
I say count it all. Everything. Including all Henson Alternative projects. Don't let legal technicalities preclude "Muppet"ness.
Maybe put the breaks on Sid the Science Kid and Dinosaur Train, given those are cgi. Heck at this point I'm going to now include Dinosaurs(tho I wouldnt count Storyteller, Labyrinth or Dark Crystal)
Recycled puppets I would say counts, including each incarnation.
Goodness knows Puppet Up/Stuffed Unstrung is recycling puppets from so many different kids shows and obscure one off productions. Wubbulous World is tough, as its part of the Dr Seuss canon. Yet, as you said, it definitely has recycled characters and is quite Muppety.
Some characters began as not being a Muppet(like Jerry Nelson's Puss n Boots) but later were acknowledged as Muppets.