Yes, I don't like to keep anything in an inbox unless I'm still working on them. I move them to other mailboxes when done with them. There may be other criteria you can use to move messages other than flags. That would depend on the criteria messages you want moved though as to whether or not it can be easily done.
I've never converted messages to appointments before. You can set it to automatically add invitations to Calendar under Mail's general preferences. If you have Reminders open, you can drag email message to it. Not sure if either of those would help you or not.
I'm sure if enough people send feedback, they might listen. There may be other Mail applications more advanced on features that might suite you better, such as Outlook. You might look into that.
You might even find extensions you can add onto Mail to enhance features you might want. That might be a better option to look into.
Good Luck