Well like everyone said there isn't really nothing I don't like about the Muppets. But if I really had to pick somethings...
1) That Jim isn't with us anymore (as others have mentioned)
2) That Richard Hunt isn't with us anymore and therefore putting an end to many great characters until not too long ago, like Scooter, Janice (as far as speaking), Forgetful Jones and so much more.
3) Randy and Andy Pig, although from, as an inspiring puppeteer myself, from a puppet standpoint they (like all Muppets) are great puppets. But from a persona standpoint I just really don't like them. They're just too dumb and not in that loveable way like a Homer Simpson can pull off. They're more like make you want to slap them around dumb,
.
So I guess that would be it. Oh and as mention what seems to be a lack of doing anything with the Muppets under Disney. Although I don't really fault Disney too much for that, cause it's not like they're too worried about doing anything with the Muppets, and really why should they be?