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There's your reason why SW fission engines can be less efficient than B5 drives.
SW later engines are less efficient, and hulls will have restrictive max engines, it's just that fission engines are the same technology. They could even share the same components, and if we add a custom pic the same pic.
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The B5 fusion engines have double the speed of the fission drives. Isn't that bad enough? 
Fission is still 24% cheaper than standard Ion Engines. And 1000% more resistant to damage but that might be to make vital comps more difficult to kill and compensate lack of shielding, so it's ok with me.
So if as you said races should be beyond fission drives by the time they meet.
Why do they have to start with better engines?
Besides the consistency issue, B5 races would have an advantage if for example two races start in the same system
I can try to go the other way and revise SW to make atomic drives == fission engines and the others a little better. But if engines have too many movements I'll pass the 255 limit in the big ships, and will have to make them use very little engines and lower their eng per move.