I have to say it depend from the playstyle of the faction.
Shields tends to produce a lot of flux when you shoot at them which can prevent the ships from using their guns to their full extent. An Onslaught armed to the teeth can charge straight on most ships and unleash hell on them. With 1750 armor, he can tank quite a beating before starting to take hull damage (and i'm pretty sure armor protect the weapons and engine from being disabled).
But with his shields on, he will overload quickly and won't be able to deal enough damage to his opponent.
In an attrition warfare (Try Tachyon style), the ships with high tech shields are more likely to win by taking their time against their opponent. But something closer to the blitzkrieg would be to the advantage of the most armored one (Hegemony) who go trigger happy without having to care about the hardflux.
You should take a look at the Thule Legacy mod. The ships are all shield-less and very heavily armored and yet can take on most fleets.
As they're completely unshielded, they also have a unique hullmod that makes them effectively immune to being disabled. Their guns and engines don't go offline, no matter how many hellbore rounds you pump into them. Otherwise a couple solid Heavy Mauler hits would render them unable to do anything for quite a while.
I don't like the idea of regenerating armor. If you want to buff then the best way IMO to do this will be to simply strengthen them.
I play on half damage everything, which is a huge buff to armor IMO, and that actually feels pretty good, so maybe something like that can be arranged
I play Full Damage because Psiyon and Okim effectively said to man up while playing Ascendancy/Ironclads respectively to provide proper feedback. Means those reapers REALLY f**king hurt. So much owies.
As for armour, I can't provide any sort of suggestion. Maybe armour hardening of a sort. Skills do it to a limited degree, maybe Heavy Armour for more armour, something like Improved Armour to less damage taken on armour. That way, your EHP goes up quite a bit without unlimiting it.
PRE-POST EDIT: Ninja'd....
Extended battles in a heavily armoured ship is not what you're looking for anyway. Heavily armoured ships are typically low-tech ships and thus rely on ballistic weaponry with limited ammo, unlike high-tech ships which can literally take the stance of "I can do this all day!". That's why I personally always remove ammo from ballistic weapons. None of that retreating because no ammo nonsense, and if the AI retreats because of no missiles, well they weren't here to fight anyway. They were just hoping for a lucky kill.