So flexibility can be reached, we just have to do it by design, and weigh the pros/cons of tradeoffs to meet in the middle sometimes.
Modularity is also big for me. I've had discussions in the past regarding another CMS you and I are familiar with Patrick, and I'm sure you were part of them. The two main points of those discussions were that:
For point one, I want to create a small, efficient core and then all functionality will be provided by Modules. I want to go so far as to create an API for the User Authentication System (Login System), so if a Site Admin wants to use a 3rd party Login Module, or their own Login Module, all they have to do is make sure their Login Module is sending the core Authentication System the proper calls and responses. That's on the Todo List ;-)
For point two, if we have an Event System then we have Events that Modules can listen to. When the Event is triggered, the Module's Listener will have the chance to step in and do it's thing. So core modification can be as simple as installing a Module, and if you want to get rid of it, you just uninstall it and the core is left untouched.
This is some good stuff :-)
I encourage everyone to create your own folder and document in the 'Our Vision' Google Drive folder and share your thoughts regarding what you'd love to see in a system like AllianceCMS!