Sins of a Galactic Empire is a total conversion; if you are going to play the mod, you must discard all prior notions and experiences of ship combat based off of vanilla Sins. If you assume, or expect, ship combat to resemble the base mechanics, than this is not the mod for you. If you want a Star Wars mod that keeps most of the Sins mechanics, Interregnum is a great choice. I'll address your points one by one.
Shields: With the notable exception of the Mon Calamari and Yuuzhan Vong ships, shield regen scales with ship strength. To give you an example, if you take an ISD and a Nebulon-B frigate at 0 shielding, it will take approximately the same time for both ships to regen to full shielding. I don't see why one would single out big ships in particular, with reference to this.
Large militias: There are certain planets, referred to as forts, which are extremely powerful planets, such as Coruscant and Kuat, which are game changers when built up. These planets have large militias as a necessity, however, there are the "No Fort" random maps which remove these planets from play, ensuring no overpowering militia fleets. Also 2-3 capital ships is not that big of a fleet on their own, even early game; you need to have a bunch of frigates to supplement your capital ships early game.
AA: In SoGE, anti-fighter frigates actually work. This is quite different from base Sins, where flak frigates are useless against fighters. Don't send out your fighters if they are in the area; either dispatch the anti-fighter frigates first, or send in a sacrificial wave to use up the flak burst(s) and hope the remaining starfighters/nearby ships can clear the anti-fighter ships fast enough.
Defenses: I've seen people use the basic turrets to take down Executors. Defenses, in the mid and late game, are generally not something that can stand on their own against a determined fleet. In SoGE you have to make clusters of defenses, with hangar defenses to ward off bombers (they have anti-fighter capabilities), a shield generator or two to make the planet invulnerable to bombardment or Auxiliary Government on some star bases, to force the enemy to engage you. With defenses you also have to consider which planets you are fortifying; a terrible desert world like Tatooine has few tactical slots and the few it has are expensive to purchase, while Fondor has a sea of tactical slots that can be purchased and for a reasonable price as well.
Capital ship levels: This is answered in the FAQ, so I'll grab the bit from there:
A number of "cruisers" were turned into "capital ships". This was primarily changed for reasons relating to how the AI handles things. Additionally, due to this, certain capital ships will not have any abilities that can be levelled up; this is intentional. If you want the full-length explanation: To start off, everyone is painfully aware of the AI's ineptitude when it comes to planet bombing. Whenever a frigate has planet bombing capabilities, it rushes to siege the planet, regardless of it's frigateRoleType (aka. what the AI uses the ship as). Capital ships do not have this problem. Further more, one can mess with the AI which results in them spamming capital ships, which SoGE has done.
Most of your points are valid with reference to vanilla, but SoGE is just such a different beast.
