I'd suggest taking the Eldar MMS and holofield rules (found duplicated in BFG:R as well).
Andy Chambers and others had some old house rule ideas that in the old old taccom site way back when. A few of them I liked such as special orders for break formation/join formation (pretty elementary sounding concepts really). In fact if I remember correctly it Andy that originally suggested the ordinance cap that eventually became the rule, no?
Our group allows escorts and ships of the line to squadron as THAT'S WHAT ESCORTS FETHING DO!!!
We've made any spinal mounted weapons such as the Nova Cannon FFw as it fits the model well. In case of Novas we've reduced the scatter a bit and fixed the holofield rules to not protect as much for an area effect style weapon (my Eldar opponents stated, "If I'm sitting down range from your novas I deserve to get blasted"). For FFw lances (eg. Dauntless we've dropped the points slightly). So far seems to balance well and prevents eldar carrier fleets of doom
Added rules for Eldar in low orbit consisting basically of sunward edge being the top of the L.O.T.
Tried once to make a true physics ruleset with inertia for ordinance and ships. Never got it to really work right though.
Also have played with an EA style activation play (plays exactly as it sounds) as an experiment. Resulted in a much more deadly game IMO.
Another interesting experiment was to lift the rules from the old ship combat game,
Alpha-Omega, where each ship's actions per turn were recorded and then played out in simultaneous form. Really changed your play style to a much tactical form.