I totally agree with you on the importance of narrative in the game, in the spirit of The Dark Wheel and other good Elite/Frontier stories. And, as you say, there are lots of ideas from those stories that could be incorporated (though in the case of many of them, including my favourite, Nothing Like The Prodigal, you couldn't "play" the story - except in the sense of visiting the locations).
Re my Taranis storyline: I intend to progress it in my third OXP - however, until the problem of getting a ship to launch a Q-bomb on cue is solved, I'm pretty much stuck. I tried for about a month, before switching my Oolite-type creative energies to JfMC. Which is close to completion...
Re in-jokes: I'm not against them in principle - the "Oo" thing just doesn't do it for me. Don't find it funny, and I don't fancy seeing "Oo"s on ships, billboards etc when it doesn't make sense within the Elite universe. Still, each to his own, and I'm in the minority
I confess I haven't played Assassins yet - mostly on account of my curious attachment to Galaxy 1 (I wish it were possible to jump "backwards" as well as forwards through the galaxies - that's one of my top three wants). But I'll get round to it eventually - it does sound very cool.
*EDIT* The Navy v Thargoid thing interests me too - intend to come at it from the fan-fiction side, though this won't be for a while...
*EDIT* In preparation for this, I've been pondering "the Navy", and have formed some very definite ideas about ranks/structure/insignia, based on what we have
here, but with a few adjustments. (For starters, no way would a Commodore ever be in total command, or the Navy would be tiny...) This is for the future, though