A specific quest line for each major aspect of the game (basic flight, combat, mining, trading, crafting, etc), able to be completed independently (after flight of course) such that a combat player could ignore mining and trading
They have actually done something very similar to what you have suggested. There are four Factions (there always have been). Each faction has three "starter" schools. If you create a character specced to be a "soldier" you will end up in a naval academy and have a tutorial agent that will introduce you to combat. If you start as an industrialist, you will get a tutorial for industry. Same goes for, I believe, mining. Any player is free to go to these schools and take the tutorials. So you are not locked in. Problem is, they don't do a good job of telling new players that all of these tutorials are availalbe, and where to find them. The starter systems are listed on some site somewhere. Really, all of these tutorial agents should show up in your agents folder. But they don't. Kind of weird. As to your other points, I'm not sure they will ever change combat. It seems like the designers want the game to be strategy based rather than reflex based. Resource gathering will probably never change to the lengths you suggest. I guess its supposed to be a timesink. And, as for skills, what new players should do, is specialize into one combat role (i.e., tackler, ewar, etc...).
You are in the hall of the mountain king.