N.B., this isn't meant to be as rude as it will probably sound, but: This post is just so wrong in terms of the physics, I'm not going to try and correct it, let's just pretend luckless' post never happened.
Doh! LOL. No offence is taken.... Ok lets try this angle, I for one wouldn't like the idea of not being able to fire weapons because we're going over a certain speed, and if we're going for turn-based combat, how do we know what speed we're going as (from a gameplay point of view) we're standing still. Of course it can be done, but it'll involve too much micromanagement (although the AI could handle some, if not most of it) that i feel will detract from the intensity of combat.
HOWEVER, i agree we more elements in combat than simply destroy their fleet before they destroy yours. The Battlefleet: Gothic rulebook contains rules on having 'special mission' each game (or combat in our case). You are given special mission such as 'destroy the admirals ship' and 'capture VIP' etc. etc. A random ship of the enemies is chosen and you can optionally fulfil this mission, and you get extra points. This is just a vague outline and would need a lot of work to fit into FO, but its just an idea for people to work with.
I like emrys view on morale (whos idea was it originally?) i think is excellent. You could have a flagship, that if gets destroyed causes a major morale loss. Lots of things really.
And nebulas were used in Star Trek: Armada. There were four different kinds (represented by different colours), some beneficial and some harmful to ships. We could implement a similar system (good for gameplay, but certainly NOT realistic!) Asteriod fields are good, maybe giving a cover from enemy weapons bonus (repesented as a percentage, and reduces the larger the ship is), but at the risk of being damaged but asteriods (also represented as a percentage, and increases the larger the ship). This would mean a group of small ships could hide in an asteriod field, and perform hit and run tactics on a fleet of larger ships. Defenders could take advantage of this if theres a time limit though and just hide its smallest ships in there until the time limits up
[EDIT] Corrected a whole lot of spelling and grammar