Regarding engine size: I tend to go for size 1 or 50, because of the way efficiency scales. We don't get much for smallish-but-not-tiny engines, the difference between big-ish and 50HS is considerable. Most of my real ships get size 50 engines. While research cost is an issue, I feel the penalty to maintenance life is overstated here:
1) For most military ships, the additional engineering bays to reach desired maintenance life take up less space than the fuel savings while still reaching desired range. Engineering bays are a one-off expense, higher fuel use continues to be a pain.
2) Maintenance lives aren't equal, those additional engineering bays aren't wasted. A single ship with a single huge engine may have a much shorter expected maintenance life than one with many small engines... but that's due to variance. Much less pronounced in a fleet-to-fleet comparison where ships can exchange supplies. If you compensate with additional engineering bays, your fleet will last longer even though this isn't apparent from the design screen.
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If you design your ships to fixed requirements like speed, range and mission tonnage, engine power multiplier and corresponding engine size to achieve the desired speed give us a trade-off between fuel efficiency (better with low multipliers) and cost/size efficiency (better with high multipliers).
Surprisingly, the default 1.0 multiplier is awkward here, because of how costs scale.
0.9 power engines cost 0.81 as much as 1.0 engines (quadratic below 1.0) , 1.1 power engines cost 1.1 as much (linear above 1.0).
Dipping slightly below 1.0 power multiplier will save fuel without a noticable increase in build cost.
Go too low on power multipliers (with correspondingly massive engines) and your fuel efficiency will eventually drop because you spend most of your fuel hauling around oversized engines and have very little mission tonnage compared to total size. Even before that, additional fuel efficiency is expensive in terms of size and build cost. I'm often fine with 60% engines, but rarely with 70%. On the other hand, most designs I see on these boards are too stressed for my tastes - I only go for less than 1/3 engine weight when compactness is very important (e.g. missile fighters which are expected to launch without being detected themselves) or I'm limited by technology (already on my lowest engine power multiplier, ship doesn't gain much from speed).
Sometimes, it depends on your overarching plan. Assume you want some properly fast warships.
If they're intended to be a fleet staple, you need to watch fuel consumption... having them consist mostly of medium-power engines makes them big and expensive for their capability, but you can actually use them without running dry.
If you intend to shove them into a hangar until their perfect quarry shows up (like a certain spoiler, which the right design will humiliate utterly), you care more about build cost and required hangar space than fuel use: less/smaller but more stressed engines.