I want to add my voice to the cause of ship module reform. Right now, ship design seems very stale and boring.
I have a slightly different take on the slot issue. The loss of granularity is a big problem, but it's not the only one. There's also the loss of racial diversity. In 3, you had the Dense trait or attribute (I forget what these things are supposed to be called) that would increase total capacity of the ships. Added on to that, you could specialize your technology to miniaturize your modules to make even more use of your Dense bonus. There were also race-specific technologies that could affect things like ship capacity. The result was a huge variety in ship designs between races. This in turn would affect the decisions you made about fleet composition and logistics. (You could choose to prioritize better ships, or bigger fleets. Since there was also a racial trait effecting fleet size, it could be a legitimate strategy with some races to prioritize quantity over quality.) The result: every game of 3 you had to adjust your ship specifications (and research priorities) to make the maximize your race's strengths or mitigate their weaknesses.
This depth is completely lost in 4. The only reason to design a custom ship now is to make sure that you are using all of your slots for weapons, with maybe some defense thrown in. You researched Flexible Bulkheads? Better put another gun on the ship. There is absolutely no diversity outside of command ships. There is the Warrior trait, but that existed in 3 also.
Despite the huge loss, I haven't lost hope for GC4 yet. The new system is easy to understand and use, and that makes it a good starting point. If certain reforms are made (like the idea of slotless modules), then I think the new system can become better in time. Another option would be to designate a certain number of slots for certain functions. Each hull size has its own base slot capacity, so you could say that there are X slots designated for weapons and Y slots for defense, with larger hull sizes also having one or two "special" slots for amplifying/extending range, etc. (The extra slots you get from technology could be totally free slots, or they could be free for anything except "special.") This would do a couple of things. First, it would solve the "defense vs. more offense" issue without requiring the developers to figure out how to balance defense and offense. People would use their defense slots because you either "use it or lose it." Second, it would do the same thing for the "special" modules which at present don't see much use. Third, the proliferation of "special" modules would increase the sense that each ship has a designated role in the fleet. One ship might be solely about damage, another might be about staying out of enemy range (through extended range) and buffing the defenses of the fleet. Lastly, it would further differentiate big ships from small ships because only the biggest ships would get multiple "special" modules. This would result in more interesting choices in ship design and fleet composition.
One last point. I was intentionally vague about the relationship between Y (the allowed number of defense modules) and X (the allowed number of weapon modules). Because I am neither certain myself what would be best, nor how this solution is likely to be received by the community, I thought it best to leave it open. One possibility would be to have X=Y; another would be to have X be less than or equal to 3, depending on hull size. This last one would be interesting because on all hull sizes except Massive it would force the player to choose which kind of defense to build, adding a layer of strategic depth. Only massive hulls would have the advantage of having all three types of defense, making them the ideal backbone of any fleet.