One thing that I noticed when playing with fighter setups is that the hull itself seems to have zero mass. All hulls seem to start with 1.0 weight (probably to avoid divide by zero errors), but that weight disappears when you equip something to the hull. What this means is that the ship itself has no mass, so the pilot is apparently flying around strapped to an engine. I did the calculations for speed / (thrust / weight) and they always come out to a ratio of 1 regardless of which hull you are using (after adjusting for speed bonuses) and what you have equipped to the hull.
Now you may ask, despite being a tad unrealistic, why exactly is this a problem? Unfortunately it encourages minimalistic setups leaving slots empty, especially for fighters (i.e. achilles fighter + engine 3 + rocket launcher). You would think that 2 engines attached to the fighter would actually be faster, but in most cases it will actually slow the fighter down and make it more expensive. What I propose is that all hulls be given a base weight, with the smaller ships being lighter and the larger ships being heavier. To compensate, all engines would need a significant thrust increase.
The ultimate goal of such a change would be to reduce the cost effectiveness of minimalistic setups and allow for a larger variety and better balance of fighters. This would also help to differentiate some of the smaller cruisers and frigates from their larger brethren.