I don't really think there are any 'space sims' in the traditional sense that meet those requirements to the extent that your query suggests to me, particularly with any significant level of [non-core gameplay] depth (micromanagement) before hitting the more tactical, space-themed RTS (RT4X) games, such as the just released
Sins of a Solar Empire. I haven't tried it myself, but perhaps
Eve Online would fit the bill? I've heard the mercantile aspect is quite sophisticated.
As swaaye suggested, games like
Freelancer and
Privateer 1 & 2 give you space sim gameplay in a sandbox environment with well-developed universes and basic economies, but in a lighter manner to what I suspect you're ultimately looking for. As you probably know, there's also the minimalist
Homeworld 1 (+ expansion) and
2 third-person space RTS's and
Nexus (as you mentioned) but they're pretty low on the extra, non-core attributes.
Project Earth is a fairly competent Homeworld clone from 2002; I think
Haegamonia: Legions of Iron veers a bit more into some of those extras, but I've only played the demo. Rounding out the more RTS-heavy would be Stardock's
Galactic Civilisations 1 & 2 (
Sins is their new baby) and maybe
Conquest: Frontier Wars.
Star Trek: Legacy,
Bridge Commander and
Klingon Academy should be full of multi-weapon/system combat -- I haven't played
Legacy or
Bridge Commander, but really enjoyed the gameplay in
Klingon Academy. There's also a bunch of
Starfleet Command games.
Privateer Online might have fit the bill, but it wasn't to be. Word is that EA have a next-gen
Wing Commander title in development...