I've seen a few different proposals for 'geared' engines or more speed options, but while I think something along those lines would be useful and flavorful, there are innumerable ways to implement it, most of which I feel would be too complicated.
So, I'll take a stab. The current speed option is nice for tactical purposes, but has few other uses. The real naval operations that serve as flavor inspiration for so many of our games - and plenty of the SF settings that do the same - feature ships that have efficient cruising speeds and inefficient combat/emergency/flank speeds. If these are to be translated over, they could be an option that is not strictly better or strictly worse than the two extremes - having high-boost ships with plenty of tankers, or having long-range commercial-engined warships that use minimal fuel.
This option, whatever it might be called, should give engines an additional operating mode where they run as though their power setting was lower - possibly a single tech that gives a 40% down-throttle, possibly a series of techs going from, say, 20% to 60%. This mode should be toggleable on individual ships, and should work strictly for military engines with a base power setting of 100% or higher. This implementation would avoid the need to change any formulas for engine power. The cost could be added engine weight - likely around 10%. Currently, a 20HS ion engine at 100% power outputs 250EP - with this design option, a 22HS engine would give either 250EP with higher fuel consumption or 125EP with the fuel consumption of the 50% power setting.
I think this is the cleanest way I can find to implement the idea.