I think this whole mess has (yet again) uncovered two major issues with how we do things in the WordPress community:

1. While all development is open, unless you make a serious effort there is very little chance you'll know about what's happening until it suddenly pops up as a new feature about to ship.
2. As the community of users grows, wide-scale user testing across all types of users becomes more important.

For those of us who follow core development and feature plugins with rapt attention, this new feature was not a surprise, but we are in the minority. Furthermore, the people this change will affect the most (the average user) are not aware of this discussion and will not know of the new feature until they come across it in an update.

I have no problems believing that early user tests have proven the Customizer menu handling to be far superior to the current system. Nor do I have any questions about the claims of critics that a removal of the current feature in favor of the Customizer solution will cause widespread confusion. And this is why I was never in doubt that those at the top of the pyramid would make sure the implementation would not be destructive, as exemplified by Ryan and others.

The larger implication here is that we need better communication across the board about what's happening. Yes, some of that responsibility lies at the hands of the users, but the major onus is on us that work on new features. Due to the sheer size of the WordPress user base it is not responsible to spring new features on them, regardless of how well thought out they are. People have an intrinsic fear of anything new, and we have to make sure any time something changes in a fundamental way that we ease them into it. This can be done by providing ample information before the shift happens.