I just got this game for early access, and one of the things I noticed immediately was the usefulness of system upgrades varied wildly, and the big, core question behind the usefulness of them ended up being the question "Can I replace the functionality of this module with more blocks?"
Generally, the most useful system upgrades in the game tend to have features that cannot be replicated by blocks. There is no block to increase turret count, no block to increase deep scanning range, as a result, system modules are your only way of enhancing your capabilities at that and the game very heavily pushes you in that direction.
Because of the limitation of systems, and the fact that blocks are not likewise not limited, this enforces a meta where you want to replace system modules by blocks in every situation you can. This destroys the usefulness of the cargo, engine, battery, shield, and generator boosting system upgrades. The Hyperspace module would also likewise be in the same boat, were it not for the fact that it reduces hyperspace recharging time, which is invaluable for larger ships.
So, we have a situation that for general-purpose ships half of the modules in the game are mostly vender fodder, which is not an ideal situation.
The only solutions I can think of, however, are to either add blocks for all stats, such as turret control blocks and sensor blocks, or add features in all system upgrades that cannot be replicated by blocks, for example, the cargo module system upgrade might shield your cargo bay from NPC scans. This would still make it specialized, but at least, situationally useful in certain circumstances.
I do believe that adding a turret control block would enhance the system upgrade diversity a bit, at least, since, for the average general-purpose ship, turret control upgrades end up dominating a player's system upgrade list because of how necessary the extra turrets are. The game even acknowleges this, since the Xsotan upgrades are all Legendary Turret Control Systems in functionality.