The updates in Vista also annoy me. One way or another when they're running they kill my performance (maybe it's Kaspersky's fault though), then sometimes a box pops up telling me that the computer is about to restart... whether I give it permission or not! I have an unhealthy distrust of Microsoft, but I thought I'd give automatic updates a chance... bad decision.
I can think of a reasonable reason to have multiple different versions: that way you can have more advanced versions that require higher end hardware. If Microsoft didn't relegate DreamScene (the animated desktop thing) to Ultimate you'd have all kinds of problems with people turning it on for no good reason, then complaining about how Vista is a resource hog. How much better would the average computer's performance be if people would just turn off Aero? (dwm.exe is using 250mb of RAM on my computer right now) My point is, if the feature is available people will enable it, if their system can't handle it they'll complain. Better to give those people a version without those features in the first place. That is why I'm using the Business version... I don't know what the Media Center does in the background in Vista Home, and I don't wanna know. I'd prefer it not to be there in the first place, that way I don't have to wonder what problems it's causing.
I guess you could solve that problem by having some kind of diagnostic system, but then you run into the issue of having the OS make decisions for the user (something I can't stand). A built in "vLite" like installer might work too... I wish I could easily turn off the indexer, firewall + defender, windows update, the sidebar, etc. during the install, or better yet, before burning the install disc.