Later, brah!
You knew SOMEONE had to eventually say it.

On a more serious note...
Every critique you touched upon are almost to the last exact thoughts I have about the current status of the game, as well.
Content missions are just... a necessity. I have never heard of a game being criticized for having too many things to do throughout the time people play it. Except from ADD inflicted folks who think Dragon Age offered, and this has actually been said, 'too much to do'.
I digress...
Optional paths to advancement, optional endgame paths for different playstyles (PvP or PvE), the ability to stumble into side missions as a reward for exploration in a game about... exploration. Really, especially with this I.P., the opportunities for a unique play experience are limitless.
I can't pretend to understand the goings on of Cryptic or why this game was released in the time frame/state that it it's currently. Likely reason? The almighty buck, but that would be speculation on my part without facts. It strikes me, though, that if the focus on content stays strong, good people like metric here would remain a player in the game.
The tooltip critique is so spot on, there should almost be a political movement to expand on it. Half of the 'complexity' of this game is lack of clarification and a simple, easy to understand description of what things are, and what they do. Sure, there's a place to have information about it's history and design reasons for those wanting to explore more about it (like, say.. a codex), but being direct goes a long way to aid in new players, and veteran players down the road alike, in understanding what your vision for the game really is.
About the missions, I admit it. I spent spent probably 10 minutes at the Transwarp gate at RA2 trying to get to the B'Tran Cluser. I had to look up why I was unable to access it, and only then found you had to be RA3 to actually go there. While getting to RA3, I still had no reasonable clue as to why we were given tasks or missions we couldn't even do.
Maybe it's a game mechanic oversight, or perhaps even a 'bug', but issues like that aren't 'well, this game can be complex', that's just a scratch-on-the-head design.
I think the greatest portion of your post, metricsimpleton, is by far your Final Word entry.
It goes back to what makes a game 'complex' or not, and what you've said pretty much completely nailed it. I truly believe a lot of the so-called 'complexity' is due to many things being in a form of unfinished state; a limbo of how the designers want to guide players through the experience, and how players want to figure out how crafting works, or what sector they're supposed to be in, and when.
I'm not one to have my hand held to every piece of game content, but in a game where a LOT of players had trouble finding Sulu (an overused joke now, but in beta and even launch, a moment for confusion for some in the playerbase), I really feel the expectation of the developers on what players can simply 'figure out' is a bit unbalanced, if that makes sense. I think it's a case of 'know your customers' when it comes to issues like this.
Overall, I found this game far, far more enjoyable and almost addicting than I ever considered I thought it would be. Like the OP, I would love nothing more than to stay in this gaming universe and play for awhile.
At this point, it's all up to Cryptic now. I've done my part by subscribing and playing. Hopefully they do enough down the road to keep myself, and indeed people like you, metricsimpleton, exploring new life and civilizations...
-Dragon