I use only 50hs engines for capital ships, since the -50% fuel use is huge. Which basically means size classes are built around number of engines; a destroyer would have one engine, for example, and therefor probably be around 6000-8000 tons; two engines would be a light cruiser at around 14000-16000, etc. It means losing an engine can be crippling, sure, but has nice advantages in fuel use. Usually I just use 100% power engines for most capitals, and 50% power commercial engines for long range armed survey ships.
For fighters, it's all about the power ratios. This is the big advantage fighters have over capital ships, particularly beam fighters, and the difference can be enormous; a fighter with equal engine tonnage will likely be double or triple the speed of a conventional ship. In fact I've been experimenting with 400-500 ton heavy beam fighters that are basically just small capital ships with high performance engines and most of the fuel/maintenance/cruise duration tonnage shaved off (or rather, moved to the carrier). On the other hand, fighter engine size isn't such a big deal; the difference between a 50 ton engine and a 200 ton engine is only a 3% fuel savings, so usually I just have a 50 ton fighter engine and assign them as needed.
Overall, I like the change. You could go with commercial engines for military vessels, or you could establish a network of harvesters and/or forward outposts and have ships that move at twice the speed (a major advantage in combat), but need to refuel more. Or something in between. It makes for interesting strategic decisions.