I work for a large record company. Everyday you'd be surprised to hear what the legal department comes up with about what we can and cannot release, even down to major songs that have appeared elsewhere recently.
Like others have said, it could be rights, royalties, or just a plain - NO. The reasoning is also this, rights given for a TV show are very specific. The cut numbers can probably air on TV, but once that medium is changed (DVD and Home Video), the rights must be secured all over again, and this time met with opposition or price gouging. It can get very frustrating.
In this respect, I can totally understand why some things were left out of, or altered from the first season.
I received my copy yesterday and enjoyed it thoroughly. I loved the fuzzy packaging. Nice touch! I thought it would have been better to have classic Muppet pictures in it rather than the the more recent versions of Piggy, Kermit, Fozzy, etc. But it's what's inside that counts. And it was exactly what I wanted, the original season 1 openers and great episodes I love and am so happy to finally get on DVD.
My advice is to thank Disney for releasing it, to encourage the other volumes to follow, but to give your input. For me, I'd tell them that I'd like scene selections within each episode. I'd like guest star audio commentary or on-camera interviews if they can obtain it. For instance, I'm sure Joel Grey and Florence Henderson would have interesting stories that would have been great to hear.
Tell them, we'd love to eventually get those cut segments one day, even if they are included as bonuses on future volumes.
The important thing is that we got what we wanted, a great collection worthy of having. For $30 bucks (give or take where you bought it at), I have more than half of what Time Life put out at a much higher price.
And, this is just the beginning...
Andy