I do agree that the whole unbundling movement happened a bit too soon, but stopping it is no longer possible and reverting to bundled libs doesn't make any sense now that it has happened and most users already installed the necessary libs. But everyone is free to handle it the way how they want any ways. I personally would have liked to wait with it until Minion 4 is ready to avoid the confusion we have seen.
stale libraries) Next game update we'll get a tiny new feature, allowing us to specify a minimum AddOnVersion for dependencies (e.g. "LibAddonMenu>=29"). That way authors will utilize the AddOnVersion, even when they don't bundle the lib and won't have to worry about old unsupported versions of libs being loaded.
lib path) One of the reasons I added the loaded addon logging to LibDebugLogger is exactly that. If you utilize it and educate users to send you the log file when they have a problem, it won't be an obstacle as it tells you which folder the libs are loaded from.
addons including libs in the root) Unfortunately I noticed some addons doing exactly that while working on Minion 4. And it's really bad, because Minion 3 will simply replace the folder without a notice and won't even recognize that the version of the installed standalone library has changed on the disk and still show it as up to date. I plan to add something to Minion 4 to handle this case better, but I believe in the long run, ESOUI should recognize bundled dependencies on the root level at upload time and deny the upload.