I have upgraded two MBP and a MB to Lion without any issues whatsoever. I have been about 98% pleased with Lion. I have found it to be a great upgrade and offer a lot of usable features. Yet, I do have a concern that Apple appears to be moving the Mac toward being more of a consumption device than a production device. Leave the content consumption for the IOS devices, because that's what they are made for. I love my iPad 2, but I would never attempt to do serious writing, programming or design on it. My MBP is great for the video, graphic and web designs that I do. It would never happen on an IOS device. (At least not now. I'm sure technology will eventually change that also).
However, I will agree on the "Versions" issue. That is a frustration. I often open a document and immediately click "Save As," in order to create a new document. I use the old document as a "template." Of course, there is a work-around. After you open a document, click on "File -> Duplicate." Then, click "Save," and it will prompt you for a new file name. That adds two steps to what should be a one-step process...i.e., "Save As." I would love for Apple to make the "Save As" as an option again.
Although the "Versions" has not been a security issue for me, I do understand how it can be for others. If you are working on a shared and sensitive document, the old versions could create a problem for you. Again, "Versions" or "Save As" should be an option switch.
Concerning the auto re-open of windows/App, you can turn that off under the "General" settings in System Preferences.
I have found a lot of the quirks are adjustible in either the System or App Preferences.
Overall, I have found Lion to be a stable and useful OS. I hope this comment has helped.