I'm not sure if the question is "Who do you want to be the top characters now?" or "Who do you think are the top characters now?" Quite a few people, it seems, put Piggy and Fozzie near the top of their list for "now," which would make sense for the first question but not the second. In terms of how much the writers use them and overall popularity, here's how I see the hierarchy:
The "classic" list:
Kermit
Piggy
Fozzie
Gonzo
Rowlf
Scooter
Floyd
Animal
Statler & Waldorf
Bunsen & (especially) Beaker
Swedish Chef
Sorry, I had to go to 12. Any less would have seemed to be a glaring omission to me.
I think Animal was always popular, even back in the old days before Muppet Babies. Quinn, you make a good point about Janice being featured more, but she was largely the "straight man" to Dr. Bob or just used in musical numbers. Animal was a laugh-getter and often useful in backstage plots, so I don't think it's out of place to rank him high. The litmus test: I can think of lots of classic Animal merchandise, such as a Fisher-Price stick puppet as well as a large hand puppet. I can't think of anything like that for Janice.
The "now" list:
Kermit
Gonzo
Rizzo
Pepe
Clifford
Statler & Waldorf
Bobo
Bunsen & Beaker
Piggy
Animal
Swedish Chef
Fozzie
This second list focuses more heavily on how much they're used by the writers nowadays. As you can see, there's some disconnect between the two lists, which may be why there's such been such a falling away of interest. Of course, since Frank isn't that active anymore, and since Jim and Richard passed away, we can't put all of this on the writer's shoulders. Also, it is good to emphasize newer characters from time to time -- I doubt many would argue with Pepe's or Bobo's rise in popularity. But I don't understand why we don't see more of Jerry's characters, and I don't think I've exaggerated the overusage of Clifford and the underusage of Frank's main characters. I think the return of those characters to the forefront (whether by Frank or someone else) could do a lot to help the Muppets' hurting image right now. That does seem to be the direction that they're going.
I'd like to see Rowlf return to this list, and Scooter to at least come back to supporting-player status. I wouldn't be averse to Sal joining this list soon, but it's too soon to tell if that's the direction they'll take. And of course, with the new movie and series, presumably more new characters will be introduced and current characters will be moved around some more. So this list is always subject to change. But this is how it looks from where I'm sitting right now.