"if a plugin developer is thorough in their development process, then they will include hooks and filters, to allow for extensibility and customization."
Right, but how many actually do that? 10 percent?
"there's no real effective way for wordpress (as an organization) to establish some sort of regulation per this."
I'm not proposing a regulation, I'm proposing a technical solution, just like with child themes. Child plugins could be activated before parent plugins, and WordPress could parse out functions from the parent plugin if an overriding function existed in the child plugin.