I'd say each of the annoyances has a historical reason for being there, but not a real reason as in "this is just the best way to do it". You make it sound like it's a cohesive platform that was designed to fulfill particular goals from the start, but it definitely wasn't.

I agree with you about the value of the web platform. It has a lot of advantages, especially from a business perspective, but it doesn't mean that it's a good platform.