Home rule 2: All important systems need to have a spare one so I am not going to use 1 big engine.
Not a bad rule, but my variant is have enough spares to repair anything, and go into battle with battle tugs, commercial ships with lots of armor, a tractor, and extra fuel because, why not?
I basically design a size 50 engine and lots of size 1 engines of different efficiencies. Possibly a size 2 if there is a cost break issue with fuel efficient engines.
My fleet speed is determined by what speed I can get out of commercial engined ships with 50-60% engine mass. However, I also have boosted ships that I can transport in carriers if necessary, at least to get them across jump points.
Part of my decision for going with commercial engines was to save fuel and engine costs, but now that I have Fuel Harvesters, I have lots of fuel. The other part was a desire to avoid having to spend more research on jump technology until I absolutely had to, and military jump engines of any size take a bit to research. Some things may just have to wait until I have a propulsion anomaly to exploit.
My strategy has been warped by low availability mercassium on Earth, and the complete absence of it anywhere in the Solar System. Once I get my El Dorado (4 jumps from Earth) in operation, my Mercassium problems go away, and I can go back to building more research facilities.