I was playing Endless Space 2 yesterday and thought, that it would be both more logical and more fun, if you could research a weapon only if you have also researched the previous one, for example get the second level missiles if you have knowledge of simpler missiles. This way there would be specialization for each faction. 


Another example: in another game, missiles and propulsion were linked in a way, that you can be more effective as a missilefighter if you also want speed. 


Right now the way I choose my weapons in ES2 is by looking at my resources. I might not understand the current mechanics, but there seems to be not much you can do to your own ship design quality if playing against unknown weapons and defences.


Specialization would really make the game feel more alive, since every save you start would be different. The way you would play could be affected by random events and also your own analyzation on your opponents weakness and strength.