Exactly, you have choices! Choices that actually mean something besides "I can afford this hull and its obviously better" or "this ship looks cooler".
Using your line of thinking, one could easily argue that the game should remove the entire skill system and just replace it with flat, across-the-board increases to stat with each level gained. This way, you wouldn't be forced to choose between going for armor hull mods instead of PD AI, or whatever.
The problem with that approach is that you end up with a game where you can easily do everything on your first playthrough. That's really the last thing you want for this kind of game; the player should feel like each playthrough allows them different options and choices, which lead to very different experiences.