I've also been playing with this and have a more positive take on it.

When you mark a message in the Inbox as read, the message is technically marked read in the All Mail folder as well, but you probably won't see this take effect until your folders are refreshed (or Mail.app is closed and opened again). You shouldn't have to manually mark the All Mail copy as read also.

To archive messages, just put them into your All Mail folder in Mail.app. That is equivalent to archiving in Gmail.

I hope you makes your experience slightly more pleasant!

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A nice way to speed this up would be to install Mail Act-On, a plug-in for Mail that allows you to add keyboard shortcuts to actions like moving messages to specific folders and other cool things.

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