With regards to complexity, that's what I like about the game, and that's what makes the combat unique IMO. There are many factors to consider when outfitting ships to make them effective, and you can tailor your loadout to be effective against particular enemies you expect to encounter. I think the game would be extremely boring if all the guns just did x damage to any possible target. Most of the interesting loadout decisions exist because of all the armor, damage type, and flux mechanics.
In terms of specific numbers, I don't really see how calculating things is relevant. You're still just going to shoot shields until they drop and then hull/armor until they die, regardless of the exact numbers. If you understand the basic ideas/mechanics (damage types, flux efficiency, armor), you will be able to easily identify which weapons to shoot at which times/targets. Even if the numbers were always the same, you would do the same thing. You're never going to count/calculate the number of pulse laser shots it takes to kill something, you just shoot until it dies, and sometimes it takes longer.
I do think it would be nice if the enemy skills were more clearly communicated to you so you could know in advance what you're up against, but I have no issue with some enemies having skills that make them more difficult.
With regards to active abilities, Accelerated ammo feeder is a ship system, it's not something that can be added to a ship, so I don't really understand how it can be compared to skills and hullmods that modify stats. It would be impossible to balance the game if powerful active systems like AAF could be put on any ship. Also, I think having active abilities only available to specific hulls is really good because ships have unique and defining characteristics that are not stats. If you could add active abilities to any ships, ships would just become stat sticks where you put the best abilities on the hulls with the best stats, which seems like the opposite of what you want. Active abilities should be defining traits of ships, not customizable additions IMO. (It's also worth noting that there's a ton of back end complexity involved in active systems like adding UI and controls so the player can use them. Thats a ton of work to add from a development standpoint).
With regards to CR, it's definitely a divisive topic in the community. However, fundamentally, it's just a resource management mechanic. There are entire games (survival games) where the only thing you do is manage resources, so I don't think it's correct to call it 'anti-fun'. There are many people (myself included) who find resource management mechaincs to be interesting and fun. It's fine if you don't enjoy it, but lots of other people do. If you really hate it that much, you can edit upkeep costs and recovery costs to your preference in the game files.
With regards to deployment points, the reason that mechanic exists is computational limits, not balance reasons. It ensures the game is playable on low end hardware. Once again, you can go into the settings files and edit the max battle size to allow for any number of ships, although it kinda messes with the new skill system and you might need to tweak those numbers to compensate.