What's wrong with a customization that's actually customizable? Currently there's not much you can do as all the variants are pretty much as optimized as they can get, unless they use the Salamander MRM which you just trade out for the Harpoon, but that's it.
that's not true, Variants are only semi optimized... to be honest, i never use the preset variants and always equip my ships how i think it suits me best, especially because PD isn't PD, you can for example use different PD weapons to save some OP and spend them somewhere else
the people who created the variants are just humans too, there is no reason why you couldn't be as efficient as they are when equiping your ship with weapons and hull mods
also... salamander MRM's are quite nice 
Graphical indicators of broken armor aren't in, you cannot tell how much armor you have left in total, only your hull and flux capacities.
there is graphical indication of armor in the bottom left, the little image of your ship, when the armor get's damaged it changes
also, your ship itself displays broken armor pretty good, it changes the sprite
any other way of displaying armor might be difficult to realize... armor isn't a total, there is no total armor
armor is directional, you have front, rear and side armor...
displaying that in a HUD will take up a lot of place, clumping up the UI
Auto-pilot is simply better in the area of weapons control, reflexes and mathmatics. Turrets in starfarer can attack several different targets whereas if you're in control they can only target what you aim at. The main problem is that beyond things like maneuvering, shield management, and other such there's little reason not to leave your weapons on auto-pilot. Sometimes the game's total auto-pilot is even better than the player, not always but it certainly can be. Especially at the 'Elite' rank, I hope you realize that there's a huge difference between the strength of green and elite ranks.
Auto Pilot is not that good, it certainly has it's place but if in doubt it's always better to control your ship yourself
Reason for that is that AI's are always limited in certain ways, Humans are way better at decisionmaking than any computer
as a human player you can optimize shield usage and positioning, flying and most importantly weapons
Yes! you have to set certain weapons on autofire, because you can't keep up with the AI, you can't deal with PD yourself
but in 90% of all cases you should control your main gun and all missiles yourself, the AI won't use that extra bit of range outside what's your "real" range, it's only sub par at stoping to fire when your flux get's too high or just to not fire because you are under attack... or when it wouldn't make sense to fire because you are already at 50% flux and can't bring the shield of your opponent down like that etc.
The AI can't prioritize targets in a way you can... it does to a certain amount but it can't keep up with you...
The AI can't tell that it is outgunned before getting into trouble
the AI will sometimes maneuver itself into a position where it is trapped and takes a lot of dmg... it lacks spacial awareness
and you have much more freedom when flying with a ship... the AI would never fly around a fleet to snipe the weak part of the fleet (carriers!)
There's a reason why big blue was able to defeat the best chess player, and that's because it could calculate 200 billion moves in every 3 minute periods.
this only is partly true, computers suck at calculating somethings
the best example are spacial relationships
just last year, scientiests made a breakthrough in fighting HIV/AIDS
this was only possible because of Fold.it, where gamers try to solve the riddles of biology by folding Aminoacids in a special developed game
Gamers were able to solve a special aminoacid in only 3 weeks, that couldn't be solved by computers designed to solve such things in 3 years
Ships also are randomly assigned a task when you set a capture/assist/waypoint/etc.
Rumor is, there is a priority list inside the game
the most suited ship get's assigned to the order
Thing is that I'm weighed down by all sorts of interesting weapons but none of the ships can really use them. Let's take the Tachyon Lance, currently only the Paragon, Odyssey, Apogee, and Sunder ships can carry it. Out of all the various ships only 4 can use it, and that's without stripping the ship of other stuff just to get the massive 32 ordinance space. So pretty much the only use I get out of it is vendor trash, or as a replacement for a damaged Paragon. Only the Medusa, Shuttle, Brawler, and Paragon ships carry the 'Universal' slots, that's a terrible selection. While the Medusa and Paragon are no doubt good, there hard to get and the other two are rather rubbish.
It's simply not possible to do something hilarious like make a frigate that has a Tachyon laser, which disappoints me greatly.
The problem is that it's too subtle and is imprecise. Actually armor is a total, each ship has a certain amount of armor on different points of the ship. So it can be quantified it just hasn't been done.
I have almost all the ships I mainly use at elite level, they're nigh invulnerable unless severely outmatched. They're only bad at prioritizing targets which can easily be fixed by issuing a 'Strike' order for your ship (Which by the way there needs to be a lot more tactical options). The only quirks I've seen with the elite AI is that they sometimes don't activate shields on minor collisions (Which do less than ten damage) when not in combat and sometimes firing off missiles and turning at the same time. Besides that they're just as good if not better at maneuvering the shields and the ship than me at elite rank. Speaking of maneuvering, try to make your ship come to a complete halt with absolutely no drift at all. You'll find this is very hard, but the computer does it all the time. While certainly not cheating, the AI can do a lot that a player simply cannot do in terms of reflexes.
That's because the AI only works within the parameters in which it was programmed. Unless it's one of those fancy AI's that possess artificial curiosity and the ability to learn than of course it won't because it cannot learn or adapt to the task needed.
There is a priority list, it however will randomly choose which is the most fit if you have say.... 5 of the same fighter or frigate. To the point where you'll have ships cross by each other because one started on the left and is heading right and vice versa which is incredibly annoying. If you try to add multiple commands ships randomly switch what they're doing.
Chesse is a finite game, while complex it is finite making it much more easy to program you dont really need AI you just need massive computing power to try every possible combination. (thats basically what the current AI is, but its getting more complex in being able to rule out options and speed up the whole process.)
At any rate, i can and do outpreform the AI on a constant basis, and alex as stated the AI has no advantage over the player meaning they set up autofires just like us and can only control 1 weapon group at a time not on auto fire and that weapon group behaves just like one manual controled by the player. Ya i cant fire my pd weapons better then the autofire can, so i let the auto fire do it... but i can most cerntainly control my antimatter blasters or larger slower rate of fires alot better then the ai can. I am better at leading fast targets, knowing when not to fire beacuse of flux issues and when to fire based on the enemies state. The AI in this game is great but it needs a bit of a tweak its really bad at sheild managment when near full flux and it also does not like to take armor damage when it should to maximize firepower.
You dont know the exact amount of armour you have left but you get a good idea of what the state of your armor is like and that is indeed a graphical indicator what you are asking for is a numerical indicator (so dont shoot someone down for saying there allready is a graphical indicator) and i think thats not a good idea as armour is not just a chunk of points that has to go to 0, there would be no meaningfull way to represent this as a number since every bit of hull has its own amount of armor so having 1000 armor left means nothing if they are shooting you where you dont have any armor left, and the current "graphical" indicator shows us where we have armor. I think adding a numerical armor indicator like you asked would confuse things and actually provide little info if any that is actually usefull.
In your 15 battles to replace a loss statement you are forgeting that you can capture ships that are now free (minus a small marine and supply cost)... Factor in those numbers when you are doing your how many battles it takes to recover calculations. Its allready painfully easy to build a giant ass fleet and i am hopeing in the next realease it becomes harder. Personaly what i would like is to be able to capture more ships but have more costs asociated with capturing and repairing them so i can get access to more ships but have to make decisison on what ones i want and what ones should be skuttled. as it sitts right now you can have a good fight and double your fleet value (or more) that seems outragous.
There is nothing wrong with having ideas, i just disagree with some of the precieved problems you have with this game.
They indeed can do things that players cannot realistically do, you need to play with the elite AI some more. The elite AI is pretty good at shield management with a few quirks I mentioned above. I found that regular/green AI was about as dumb as bricks, but the Elite AI was about as tactical or better than I was, even possessing good flanking ability.
Even if that is the case that they can only use one at a time, that doesn't mean they can switch between weapons within a few milliseconds of each other.
As for how armor could be better indicated?

Currently armor is either Green or Gray, some more variations between those points would help tell you how much armor is left. Could start as blue (undamaged), green (>75%), yellow (>50%), orange (>25%), red (<25%) and grey (0%).