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That's quite a simplified explanation which sidesteps the issue of properties that correspond to attributes, which is where most of the confusion is going to be. And I totally disagree with your description of things like Boolean attributes/properties as "weird edge cases": their behaviour in most browsers is well-defined, consistent and not really at all weird, particularly if you limit yourself to using properties rather than attributes, which is almost always the correct approach.

Saying that it probably won't affect existing applications is just misleading. 1.6 fundamentally changes the behaviour of attr(), which is a very complicated and commonly used method. Furthermore, there's really no point in this if you're not going to encourage people to move to prop() rather than attr().

The messages coming from jQuery about this change seem very vague to me. If you're going to spring this kind of change on your users then they need to understand what it is that you've changed and why it's a good thing (I think it is, by the way), which one documented example and a hand-wavy assurance that it might probably be mostly OK doesn't do.