I agree with pretty much everything said here and I'd like to add that I think they should add in the sense of "dungeons." Or take EVE Online for example where you have "rooms." Or Destiny's "raids."
You should be able to (and with a group of people / wings) go to a USS and have it (and of course this can be random) spawn an event that takes you to different locations. So that you aren't just always simply in the open. So you can use structures to evade and hide behind, etc. ... And what about blowing up structures??? It only seems like you can blow up ships in Elite. Why can't I blow up big structures?
There should be randomized and procedurally generated "mini events" that can affect a system just like regular boring missions.
Of course you should also see bounties on these NPCs in the dungeoned events. This (along with being able to do it with a group of people and split bounties/standing boost) would make the game wicked wicked awesome.
Even if it cloned a lot of Eve's gameplay in this regard. Could you just imagine a clone of Eve's system but as a 1st person combat sim? WOW! I don't care if it had all the same graphics and jump gates and ripped it off completely...Just taking that enjoyment and putting it into the dogfighting of Elite would be EPIC. Plain epic. Frontier would really start to pick up new players and convert many PvE players (of course Elite also needs more items and such - like rare/named items that you can't buy but can earn or scoop up).