Ignore the green name and title text for a moment while I put my $.02 in on this matter. Although I find the versioning differences to be a pain as well between the two clients, this is easily overcome by taking a few moments to load them side by side and tweek your lists. I did this and am quite happy with the results. Some addons I have curse exclusively update while other I have set up with Minion. My preference is based on which site I think a particular addon is updated most at.
I strongly urge anyone who uses both to take the time to do this. It will cause a lot less headache for you in the end. No one can force an author to use the same version scheme across all the sites; It's their choice. However, you have the ability to work around this. Think of it as configuring an addon for different toons.
Oh, and before it comes up, I run about 150 "addons" (quoted because I'm not excluding individual "modules" at this point, such as AtlasLoot's) and it took me about 10min to do this. Honestly, if you are running above this number you probably need to sort through them anyways and get rid of those you never/rarely use. Just a thought...