I agree with all of this :) Meteor is self-contained and installing it in /usr/local is totally optional. The reason we install into /usr/local is that it is a way to get the 'meteor' command into the user's path without trying to edit their dotfiles for them, and without setting obscure system preferences that the user would have trouble unsetting. We went to a lot of trouble to make it easy to try Meteor, and we thought that "great, now go edit your dotfiles" would have lost a lot of people.
If you don't want it in /usr/local, you can check it out anywhere you like and just run the 'meteor' in the top directory of the checkout, and it'll work great. This is mentioned in the README/on Github, and it's how we have been developing Meteor. You can have as many copies of Meteor on your system as you like, and they can even coexist with a copy at /usr/local. So for me, I type '~/co/meteor' to run the meteor that I'm developing on, and 'meteor' by itself to run the latest official release.
You can either build the binary dependencies (node, etc) yourself by running an included script, or if you do not, the first time you run meteor it will automatically fetch a prebuilt binary kit for your convenience. All of the binary dependencies are kept in a directory in the checkout and managed by meteor, meaning that each meteor install on your system can have its own version of node.
Finally, to your last point, 'meteor bundle' does exactly that :P In fact, right now on our deploy servers, we have live apps running that were deployed with a variety of historical versions of meteor, all coexisting side by side.
I'm sure we'll have to revisit all of this as the Meteor ecosystem gets bigger and more complicated -- when all of the packages do not fit in a 'packages' directory, and when there are more binary dependencies than node and mongo. But I hope that this helps to persuade you that we're not totally nuts, despite how sleep deprived I was when we recorded that screencast.
If you thought this was a helpful answer, could you repost the question on Stack Overflow (with the 'meteor' tag), and drop me an email (address is in my HN profile?) That way I could repost this answer there in case it might be helpful to other people.