Disagree on cloud lightning. I've always found my fleets closing to melee range. And on crystal plating I just don't think thats going to get you as much value as armor given that is impacted by repeatables. In fact I don't see how its possible mathematically for you to get more out of crystal plating when you can use armor with like 60x repeatables. Thats +300% HP. As for the cost point the other poster made, not sure cost matters when you got a 2k alloy income. OP can afford to put cloud lighting on his ships if he wanted to.
Also, as to the other poster, 41k science at that date is standard for the 25x crisis so I don't know why you would assume OP is not asking for advice in good faith.
You have two choices: expect melee or dont. If you go into melee against 25x crisis you can expect to win 2, maybe fights before your fleet is completely wrecked from 25x crisis insane damage output. If you use the colossus range bonus and pump everything into offense you completely mitigate the crisis 25x damage boost and take 0 losses. You need a larger fleet and more techs to pull it off but its more efficient if you include replacement costs from losses in melee in the comparison. Especially vs contingency where you have to fight at least 5 large crisis fleets I consider it the better strategy.
You only have 60 armor repeatables if you actually go for them. When crisis is your only concern (talking singleplayer) going for kinetic damage repeatables will be more efficient if you dont know which crisis you are facing. In my minmax runs I like to prepare for unbidden (kinetic only loadout) and refit the ships if I see signs of another crisis: Arc emitter without cloud lightning vs contingency or energy only vs scurge. If you dont know what you are facing just go giga cannon + neutron launchers and be decent vs everything and efficient naval cap wise.
If you know from the start you are facing scurge (like set it in the game options or forcespawn) going armor + energy weapons is the best, i give you that, but its not far behind going energy weapons only. Same as going shields + kinetic only vs unbidden. I just feel going for both weapon repeatables gives you more flexibilty to counter your enemy
The most important part is (as op said) upkeep which is directly affected by alloy cost (not crystal cost though), so crystal hull plating is essentially free. While it will not block large shots, some smaller missiles, strike craft shots etc will be blocked by it. But yeah its not good for defense, its just better than nothing and free. As the "over the naval cap" is just the percentage you are over naval cap you can view it like this: if your arc emitter/crystal battleship costs 750 alloys you can go 100% over your naval and pay the same upkeep per ship as a 1500 alloy fully armed/armoured battleship costs without going over the cap so the 1500 alloy battleship needs to be alot better to be worth it. Every slot you fill for a battleship needs to be important. I would even suggest going for engines 1 to lower cost, prevent the battleship from charging in (also carrier computers are often better than artillery computers here) and use mainly jump drives for movement.
Also in my other posts I always said OP is doing fine, im just sharing my thoughts on the few percents that might still be improved.
In terms of "casuals explaining the game to minmaxers", I also consider myself a minmaxer and beat 25x 2250x crisis (earliest spawn I got was in year 2260) with only about 10k science output, so take it as you will but ive tested my share of loadouts.
If you really want to minmax to the max though, building battleships is not the way to go. Instead get menacing destroyers which can refit in 1 day to counter any crisis perfectly, cost so low upkeep you can go 4x-8x over your naval cap, have insane tracking, can evade high-range crisis shots and are easily replaced even if you lose all of them.
