Muppets Tonight had so many great characters (and a few bad characters, though some fans may think differently regarding whether certain characters were great or annoying), but part of the problem was that they had so many new characters at once and so much focus on them over the classics that we knew. In fact while a lot of us felt that way, I don't think I've heard of any instances where a casual fan or reviewers cited that as a negative point about the show (though according to Jim Henson: The Biography, critics disliked the new characters from The Jim Henson Hour). I can imagine casual fans tuning in hoping to see their favorite characters and possibly being surprised, at the very least by Kermit not hosting, wondering who Clifford was, and at the very least surprised that Miss Piggy and Fozzie weren't used that much (though of those two I initially only noticed Fozzie not getting much screen time).
At the time Muppets Tonight premiered, I didn't have the internet, so there was a lot I didn't know (in addition to a lot that I did know). By that point I was really just starting to know that Frank Oz had a directing career but didn't realize that it interfered with him performing the Muppets. I knew Jim Henson had died and suspected that Richard Hunt had also, but didn't think they were avoiding recasting (the three biggest Muppet productions to have come out after that were productions where the Muppets played roles, which seems to make it natural that certain main characters wouldn't have sizable parts). Kirk Thatcher and Jim Lewis have both said that they thought of the show as a "next generation" series and that introducing many new characters was necessary. In The Muppet Mindset interview with Kirk Thatcher, he pointed out that new characters were introduced all the time on The Muppet Show (though it seems like new characters were scarcer in the last two seasons, where most new characters, even ones that weren't made from Whatnots, only appeared in one or two episodes). That got me thinking about Sesame Street: For awhile, I had noticed that there had only been a small number of new characters in the past several years, but then I started thinking that for about the first 31 seasons, there were new Muppets introduced all the time on that show, and then the creation of new recurring Muppets started to drop within a year of Sesame Workshop buying the Sesame Street Muppets. Makes me wonder if Henson was more interested in creating new characters than Sesame Workshop, or if the Workshop felt they had enough characters by then (there were a fair number of new characters within the first couple of years after the change in ownership - Lulu, Little Murray Sparkles, the Monster Clubhouse cast, Curly Bear, Cousin Monster - but with the possible exception of Curly Bear - I'm not sure how often Baby Bear's family has been used in the last few seasons - none of those characters lasted). Of course there's also the fact that shortly after that Sesame Workshop changed the format to include many recurring segments needed for every episode (or every other episode), many fairly long and only featuring a handful of familiar characters, and then shortening the number of episodes per season to 26, which might make it difficult to find time to introduce new characters.
Back when the new Muppet show planned for Fox was announced, press releases said that it would have new characters. I was thinking that The Jim Henson Company "knew better" at that point about having more new characters than old characters, and at this point the company was starting to recast Scooter, Rowlf, Dr. Teeth, Janice, and others, but I had worried that the mention of new characters meant that they'd be featured more than the old characters. But then recently the pilot script leaked online, and there's not really any new characters in that script. I don't really know what to make of the pilot script... There are good things about it, but also a lot that wasn't that great.
There are so many theories about what caused Muppets Tonight to be canceled, some more likely than others, but Kirk Thatcher recently mentioned something that he thinks might have contributed to it: At the time, ABC got a manager who was mostly interested in shows that brought in males aged 18-35, a demographic that likely wasn't going to be too interested in Muppets unless they had kids.