This problem seems to indicate a tremendous failure on the W3C's part to anticipate the actual consequences of vendor prefixes, or if they actually anticipated them, a failure to act. Despite the fact that Quirks Mode is not identical, it is a similar enough case (And one that should be familiar to every browser vendor) that ignoring its example when considering vendor prefixes suggests either willful ignorance or an extreme desire to hope for the best and ignore the consequences.
It's bad enough that -webkit prefixes are putting Mozilla, Opera, and Microsoft in this position, but imagine what this situation could be doing now, or could do down the road, to innovation in this space? If history repeats itself and we end up with a browser monoculture again, how can a new contender enter the browser space if pages are full of badly documented, unspecified vendor prefixes?
From the outside, vendor prefixes look like they originated as a passive response to the slowness of W3C standardization and the behavior of W3C participants. When you look at some of the W3C minutes - http://lists.w3.org/Archives/Public/www-style/2012Feb/0313.h... as an example - they are full of examples of participants who either do not realize their lack of knowledge or are actively attempting to hinder discussion. If it takes months or years to standardize a basic feature, should it be a surprise that frustrated browser developers roll a feature out behind a vendor prefix and the entire web adopts it as a de-facto standard? The presence of these vendor prefixes should have sounded alarm bells for everyone involved in web standardization, and action should have been taken to address it then and there. At this point, I'm not sure anything can be done except to attempt to reduce the damage.
As a web author, dealing with prefixes is miserable. Each vendor version of the prefix might have different accepted values or even have a slightly different name, and I have to go through and manually test in each browser. If I make changes to my CSS rules, I need to ensure that I update them all to match and deal with differences in syntax. The documentation for how to do this is spotty and it introduces a ton of room for mistakes in what should have been a simple part of the web development process.
As a user, prefixes are a disaster. I've got a fairly recent Android phone, and because Android is a fragmentation trainwreck, the stock browser on my phone is outdated and buggy and doesn't support lots of modern web content. To deal with this, I installed a third party browser from the Market, and I can use it to view modern web content successfully. Unfortunately, a large number of the sites I visit mess up useragent sniffing and serve me webkit-only CSS or even webkit-only JS. I don't have any options here; I can't surf the Real Internet on this phone.