No problem with the tone, guys.. I tend to do the exact same thing myself. And thanks for the comments.
I do think Sins as is works fine. However, I think the game's combat, as a whole, is overly simplistic even with the existence of many complex systems. My feeling is that strategy in play comes from interesting relationships between entities, and not simply the existence of complex systems. Theoretically, if you can keep interesting relationships while removing complexity, the game will not suffer. Complexity often can lead to interesting relationships, but if it does not, I'm happy seeing what happens when you remove it.
I got most of my early-scale changes working last night, and the result is promising, though the game does play much differently:
Since you have to tech up to capital ships, they're valuable and a bit scarce until your economy is rolling. However, you get the light carrier, escort cruiser, and siege frigate at tech 2, while the akkan & kol are tech 3, and the sova and dreadnought are tech 5 (these are simple 1:1 replacements of original ship techs, I'm going to redo the tech tree when I worry about balancing).
There are no restrictions on how many capital ships you can have, and it's certainly doable to fill up your fleet cap with lots and lots of capital ships. The capital ship crew cap certainly helps to regulate the amount of capital ships, but I'm interested in how it plays without the hard limits.
The early game as TEC is a bit of a "million frigate march". Scouts have autocannons and are good against frigates. Cobalts are good against all ship types. Siege frigates can use their missiles against planets or ships, but they aren't very effective against lots of frigates (antiheavy damage, long cooldown, though damage is high).
The escort cruiser has a beam cannon that's good against capitals (cuts through shields), an ion cannon, deployable missile battery, and a flak burst. It's a bit overloaded, but it's nice to have a multipurpose cruiser. The light carrier carries two squadrons and can use repair drones. Interceptors are good against strike craft and passable against frigates while fighter/bombers can fight back against fighters w/ missiles, kill frigates, and kill capital ships.
The armor/damage type rebalancing is more intuitive and effective. Damage type is tied to the weapon, not the unit. So, the Kol battleship has an antilight weapon (autocannons), anti medium (lasers), and antiheavy (beam cannons). autocannons are best against frigates, lasers are good against all ships, and beams/missiles/torpedoes are best against heavy armor. Some weapons ignore shields, making them really hurt capital ships. Capital ships, with heavy shielding, are all but immune to light weapon fire. By simplifying this system, the effects on combat remain similar but the usefulness to the player is increased. It's easier for ships to exploit firepower differences now.
Shield mitigation is out, but with increased armor (and increase-armor-to-effective-hp value), battles still last a good amount of time.
The capital ship shielding dynamic is fun, as some weapons really do put the hurt on capital ships (siege frigate missiles, escort cruiser beams, battleship beams)
Most importantly, all ships are viable in combat (except maybe the colony frigate). Capital ships are hardcore but have weaknesses. Combined arms fleets are useful simply because the ships complement each others' weaknesses. Combined arms in vanilla sins is simply having combat ships escort the spell casters and planet bombers.
However, in this mod, the combat results are much more decisive, and depend on your local unit type advantages much more than vanilla sins, which is more about having lots of the basic combat unit.
I will agree that by cutting out unit types, fleet composition is simpler. You have three types of frigates, two cruisers, and four capitals, and you can only combine them in so many ways.
By combining roles but still allowing ships to have a good amount of firepower, I think that increases the strategic depth of the game. With hyper specialization, your player choices are limited as there is only one type of unit to accomplish your goal, and only one type of unit that your enemy will use to accomplish the goal. With increased ship flexibility, your enemy may try a similar strategy but using different unit types
The game start is less interesting without a capital ship to level up, and the lack of the capital ship features are really obvious when playing. I find it fun to level up a capital ship, protect it, get XP, get the abilities I want, etc. But in terms of the actual combat, I don't miss the system as a whole. I also like not having to worry about how a caital ship's level determine's its combat effectiveness. A cap is a cap, and it hurts, and has weaknesses. I'd rather focus on that than worrying if my level 5 Kol can stand up to a level 7 Sova.
I like the stated idea of having ship specializations within the classes, where research adds functionality to your basic core class. I don't think we can add weapons through research, but we can at least add abilities...
The AI is smart enough to take advantage of the units & their features (smartly building good numbers of cruisers and carriers), though sadly, they do not use ships in the scout role for combat. Pity, because the arcova is now quite capable of handling itself against frigates.

I like the mod so far. I'm interested in exploring the research tree, and also changing core game dynamics between the sides (like changing how culture, trade, and mining operate).
Bugs/annoying things:
-Sometimes it crashes.
-Capital ship pathfinding/formations are buggy, as the game tries to cram too many caps into tight formations (since capital ships are frigates now)
-Not having a cap at the beginning of the game makes capturing planets slightly more difficult.
I'm going to clean things up over the weekend, add in the other two races, and probably release the mod on the forums. It's somewhat balanced, but I'm sure there are huge holes, and I'd like to get feedback. (also no more lrm rushing as TEC lololol since the lrms are gone)