I agree with the conclusion that WordPress developers could use more "rules" when developing.
But there's really nothing keeping you from defining your own rules and working within the WordPress system. It's not MVC, but you can get something as good by keeping frontend-related code/templates in a theme and backend-related code/modules inside of plugins.
The problem is that 3rd party plugins you use might not use your rules. So the code you are getting for free (or cheaply) isn't coded how you would have liked. Code it from scratch or re-factor it to suit your needs. If you were using another framework, you probably would have had to code that functionality yourself anyway.
While I'm at it some more pet peeve's RE some common complaints:
* Everything is in functions.php. Cool, so setup YOUR functions.php like this:
require_once("includes/config.php");
require_once("includes/settings.php");
require_once("includes/helpers.php");
require_once("classes/class.myclass.php");
Problem solved.
* The posts table doesn't support my data structure. Awesome, just add your own table and add a class wrapper to push/pull data. Add methods to search or whatever you need. Sure this may be slightly easier with other frameworks because they do a bit of that for you. But if you've done this once before, you just copy and paste the code and change the object names, etc.
Maybe I'm wasn't disciplined enough when I used PHP frameworks in the past, but with all of the structure and rules, I found myself wasting as much time working around those constraints in special situations as I was saving using their module scaffolding/etc.
I think this is apples to oranges comparison due to differences in prices. Early cell phones cost much more than boom boxes or CD players and they carried a monthly fee with them.
It's open to the public [oops, I lied. It's private beta] in beta: http://atlas.labs.oreilly.com/