Charles,
First of all, welcome to the Kaleidescape owners' forum, and to ownership of what is, in my opinion, one of the quintessential home entertainment devices on the planet.
1.) I think you may want to create some Collections. You can use any of the names you have listed and more to describe the contents or the theme of a given collection. Multiple collections may contain the same title. For example, Mr. and Mrs. Smith may be in a Collection called "Brangelina" and one called "Action".
2.) You can set viewing limits with a pass code. Anyone who doesn't have the code can not view things at or above a certain rating. Not sure about locking a Collection.
3.) I think overall that the Yamaha AVENTAGE lineup offers a reliable, high-performance package. I don't know what, if any, control system you have, but the AVENTAGE receivers offer control via IR, RS-232 and TCP/IP, and have some great features for a customer or custom installer to use, including Scenes. If you pursue them, and get the RX-A2040 or RX-A3040, it is no more than a firmware update away from Dolby Atmos capability. Of course, your Kaleidescape can already provide the Dolby Atmos audio via HDMI, so you're ready to go as soon as you load some Atmos content, like The Hunger Games: Mockingjay, Part 1, for example. I have just received my RX-A3040, which replaced an older Anthem Statement D1, for the purpose of having Atmos in my demo theater.
4.) You cannot back up the contents of the built-in drive if you've imported the movies from DVD locally. I don't know if you bought a grandfathered unit or not, so importing DVDs may not apply to you. If you are a convert to the Kaleidescape Store, which I hope you are, then all the content on your account will be stored for you in "The Cloud", so in the event of a catastrophic failure, you can just re-download the content. Honestly, that's the smart play at this point, in my humble opinion.
5.) I do not think the Blu-ray Disk Association will ever lift the restriction. Again, if your C1 isn't a grandfathered unit, it's a moot point for you, unfortunately. Also, in this case, the Kaleidescape Store (and Ultraviolet via Vudu or Flixster, etc.) is your friend.
It is a bit of a new paradigm, buying movies from a remote server instead of physical discs, and keeping your backup there, but I feel certain about one thing: K's server ain't goin' down anytime soon, so I would much rather have the backup of my collection stored there than just about anywhere else on the planet.