Okay I am not an addon author, I am simply an addon and Minion user who just took the time to read through this entire thread. I think my slight coding background has allowed me to follow the problems involved closely enough to understand all of the arguments on the table. But I think it is important to identify myself as a user before I say anything else.
Personally, I think if you're going to do something than do it right. We all waited for Minion's release like crack fiends and now it is finally out and in "beta". However, we have only see 1 update release during the beta and there are obviously still a lot of problems with it. Now I am grateful for having Minion and the time that Shirik and others put into it, but I think that the project obviously isn't done. It scares me that the words used about fixing problems is they might be fixed in a "future release". Now the words future release make it sound quite a way off, maybe this is completely untrue, but the wording gives off that feel.
We can't have an update program that doesn't know what files are updates and which are old. Period. However, the reason that Minon is in this current state is because of the varied versioning systems that addon authors use. So it is a complex problem and I am aware that Shirik sorta has his hands tied.
So let me say that as a user I represent a big portion of the user base that wants a working automatic addon updater. I would think that this would stop the groveling over versioning systems. The arguments I have seen from addon authors in this thread so far have seem quite selfish. Because the argument is that a standardized form of versioning would eliminate the current problem and some of you are still not willing to make the change. If you want to use your own version numbers, etc. Then make a spreadsheet on your comp that lists your version numbers next to the standardized version numbers. And when you upload use the standardized.
Now, I know some people might reply to this and be like wow you jerk, these guys are doing this for little or no money, and in most cases the latter. So cut them some slack. But honestly, I do. I don't complain very often. But I had to say something on this issue because the only argument for using your own versioning system over a standardized one when releasing something to the public is that you are OCD or lazy as the you know what.
Please guys I found this on wikipedia:
http://en.wikipedia.org/wiki/Software_versioning
See if the community can't come up with something that is more standard.