There might be some rights wrangling going on - i notice the 3 original Muppet movies are out of TV distribution but the later ones seem to be getting broadcast. Can't be a Sony/Disney thing so perhaps its to do with the Hensons. Unless Disney just want more money than Henson did.
As for Disney Stores, it seems more a supply and demand issue, maybe marketing too. The stores are in premium locations, the foot traffic is mostly young kids, so with the cost of the space they really can't take a chance and need to sell masses of current stuff like HSM, Hannah, Pirates etc. When Disney first bought the Mupps, the UK stores were full of plushes, stationery, clothes (no Pepe though) but the kids just walked past. How is a 6 year old supposed to know the Muppets? Disney of course made no attempts to promote the Muppets to them, or put any of the shows on their channels. Yet, it would have been judged from that time that they just flopped due to lack of popularity - crazy! Ideal solution would have been to have Kermit visit some stores, put some Muppet clips on the video walls - instead they use it to try sell tickets to the parks and nobody is going to spend thousands of bucks on whim so thats stupid.
The Disney Store does seem to be moving away from stocking the classic stuff. As you say, now no Muppets, lack of Donald etc. Even Mickey stuff is gettting rarer. In the UK the shelf space is even smaller now as they are trying to turn all the Disney stores into park like "experiences" so the parts of the store that used to stock the retro stuff are now turning into fairy walkways leading to "Disney Princess", and the video wall is now 360 degrees with capsules whizzing around it showing off HSM dolls while the movie plays. I'd rather they just had a good range of stuff to buy from all the brands - if i wanted to see the other stuff i'd go to the parks or cinema.
Things are starting to happen, i'm sure the Muppets will get re-introduced but if they were really going to bring Muppets back in any major way they are going to need to do a massive re-launch across all media. It's no good teasing the kids with Kermit in Mr Majoriums Wonder Emporium if they don't follow it up elsewhere - they always miss the spot. You seem em on TV, there's no merch. You see the merch, there's no TV - or they randomly appear in Disney Comic which must have confused the heck outa most kids, lol. Not sure whether enough kids would be bothered though even if they did make em a priority and invested millions for 2009, i can see they are a good solid family brand that will always be around but as for globally re-launching them - it's such a risk, much less of a gamble to just keep doing CGI rat movies and stuff.