1) You can safely ignore the bonuses from perks in terms of gameplay. The game is completely fine without the bonuses. You really don't need to know that you do Y damage with perks and X damage without them. This is overthinking it and making the game less enjoyable for you.
2) You shouldn't be using explosive damage for anything except PD. It is terrible against everything save hull. Its only saving grace is that you can basically operate at or near maximum firepower all the time while keeping shields up. However, using a mix of anti-shield and anti-armor will just be more effective overall. So I'm not telling you that you're doing it wrong, but a 5 thumper + vulcan cannons enforcer probably isn't going to work as well as an enforcer with, well, pretty much anything else.
3) In terms of ships being faster/slower, this more boils down to class. Smaller class ships can almost always outpace and out maneuver larger class ships. If you care about speed, play phase ships. They can chase down everything due to how P-Space works. You can also just use massed carriers since strike craft are super-fast.
4) Passive fleetwide buffs are important if you're going for a large fleet of ships. 27 combat ships + 3 utility ships will benefit greatly from the fleet buffs. You flying around with a single combat ship with 3 or more utility ships probably won't benefit all that much from those passives.
5) Combat Readiness exists to penalize people for using overwhelming numbers for no real reason. It also exists to penalize you for running around with a fleet of battleships. Imagine flying around with 27 Dooms. You're invincible. Those cost a lot of supplies to keep going. Same thing with battleships. Want 27 Paragons? You got it! Hope you can afford it!
6) If you're flying around in a mega-ultra-death fleet of slow battleships, no one is going to pick a fight with you save faction detachments, and they're probably just going to dogpile you with every fleet in the system. Smaller fleets can and will just avoid you. So...get some marines and go raiding. Take on space stations. Force them to fight you or else. Also, if you're pirate hunting, the pirates tend to hang out near the outer jump point. Enjoy!
7) Imagine if every single frigate pirate fleet decided to pick a fight with your mega-ultra-death fleet. What a pain that would be. Billy with a hound looks at your fleet of 27 paragons and says,
"Na bruh, I got this!" It is much better this way.
You can have your 30v30 paragon fleet v paragon fleet battle if you want. You probably need to install a mod that allows you to have infinite deployment points. The deployment point system partially exists to counter lag since the engine the game runs on is incredibly archaic by today's standards. Game's good, but the engine is old. Old engines have somewhat extreme limitations.
Your criticisms are fine; however, what your criticizing exists for a reason. There are mods that "correct" these areas of criticism. Go install them and have fun.