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Basically most medium sized ships will have 6 engines and 6 engines per move, so each ion engine (with 6 standard movs) gives 1 mov and work very similar to the original game.
Small ships will have less than 5 engines per move and move faster with fewer engines and I got tired of adding 255 engines to a massive ship with 255 engines pre move so I just gave the large ships 5 eng/move and 2 engines.
May I suggest you return to the <big number> of engines per move for large ships? What you then can do, to avoid adding a <big number> of engines, is make a new component, some thing like:
Capital Ship Engine:
-100KT size
-200 hitpoints
-65 standard movement points
Basically, just a 10x scaled up engine, with a +5 movement point bonus due to efficiencies of scale.