Hmmm... this idea could be brought further and just make it all computer functions built off of basic missile, beam, and cannon physical systems. For example. I could spend 5-20% on converting a missile to have a secondary effect such as Shot-gun, higher rof, lower rof, or even invest in multiple of those so you could make a cluster nuke for example. Then,you could add on a targeting system,: 10% for fly-by-wire, 20% for Heat-Seeking, 30% for lock-on, or 50% for instant-lock-on, etc. Then sink another 10-60% into making it a faster/longer ranged missile system. Then use my remaining points for "warhead" stuff more like current terciaries (explosive, pierce, punch, overdrive, ion, stop, etc).
Balanced right, it could lead to a lot more options than we have now instead of less; so, that things that are currently always useless, might find use through min-maxing and vice-versa. The same system could also be used to make beams and cannons more fundamentally different than one another if their options of upgrading are different. For example, give beams more options for controlling tic distribution and subsystem targeting priorities, and maybe cannons have more options for damage distribution and anti-defense-chamber options.