The main point is you don't get cluttered with lots of gizmos that do the same thing.
SE4/5 modeled each of these effectively I think but my concern with weapons in general was besides the incremental upgrades (version 1, 2, etc.) some of the actual distinguishing characteristics of the weapons was to me too minimal - been a while since I played either but off the top of my head a uranium cannon, beam cannon, and meson cannon were all very similar. The meson cannon was a little lighter, the uranium cannon required you to budget for ammunition (vs energy), and the beam weapon had a slight range advantage. Torpedo weapons were always better then missiles but the variances in Torpedo's too subtle of a nuance. I don't want to have to study weapons tables (Excel spreadsheets) looking for +1/-1 calculations - just think the advantage/disadvantage of one or the other should be more well defined for building and strategy.
One thing a friend of mine came up with (over 10 years ago) was a pen and paper space campaign/combat system.
Nothing too unusual about that except one of the neat ideas it had was players could custom design there missiles.
It was very simple I won't bother going into details unless people are interested but it was a lot of fun not only designing your ships but also designing the missiles. It added loads of depth to the combats very little in the way of extra design time.
I remember drones which you could add warheads too and use like a kind of missile - but the missiles (always preferred the torpedo's myself) that you could build into a ship were more fixed from what I remember.
The biggest thing I hated about the drones was you couldn't use them like a UAV etc. and arm them with "ship" weapons - I might be recalling wrong as it has been a while since I played SE4 - but I would like in SL to have an autonomous (no crew) in-system only drone platform that would be bigger then a fighter but much smaller then even the smallest of ships.
I don't remember if drones could carry ship weapons in SE4, but they definitely could in SE5... made 'em pretty darn powerful!
Actually, I think they COULD in SE4, it's just that they were hardcoded to ram, so they wouldn't get to fire very much before they died; SE5 let you assign other strategies to your drones!
__________________
The Ed draws near! What dost thou deaux?
They had the same capabilities in SE4 Ed. They didn't have the fire rate of a ship for missles carring 'direct fire' warheads. Anti ship missles would 'Ram' and you could even put drones (like a Multi-Warhead) on the missle. Due to the three turn re-arm cycle. They weren't too effective.
Because of their superior speed on the tactical map I always found drones without any weapons or warheads were best used to blockade the worm holes/warp points. Enemy ships would just chase them around until one or the other ran out of resources.