I think the problem is (again) the assumption that speed is an ever-expanding technology (every few turns, your capabilities increase by, say, 25%). I believe this is largely unrealistic, and even more importantly, not that fun.
Exponential and linear progression within the tech realm are hard to balance in a fun way. I tend to prefer games where upgrades get harder and harder to acquire.
For example, in many RTSs, there are few updates, and they tend to increase your capabilities by a very small margin, but the costs increase much faster.
I've discussed this in one of your earlier threads (last year I believe) but I'm much more into 'logistics' than 'science'. I assume that all of the techs already exist, and its always just a question of investment.
Can I live with a scout that goes at 50% of the topspeed? Can I live with even slower freighters? What are my interceptors?
Ultimately, my choice of engine on each ship supports its key role. Trying to fit the best engines on all ships makes you more mobile but drastically reduces your capability to build more ships.
why is speed a factor in space?
Technically, you could accelerate 'forever' but rocket science actually determine there's a 'topspeed' which is determined by the amount of fuel you have, its mass, and how burning that fuel grants you speed. Until we use a different source of energy that is infinite and doesn't have mass, we're bound to these rules. That being said, there have been interesting experiments that use other forms of energy (stars' light). The problem is that these generally tend to provide much less maneuverability over short distances, making them less ideal to be warships, but perhaps good enough for cargo...