The other thing the cutscenes emphasize, almost more than anything else, was the hubris the ancients had (which is probably why it took them so long to learn anything about the Shivans).
That's true, in the final cutscene it is stated the Terrans "learned how to survive" in their war with the Vasudans.
The Ancients likely never faced a species equal in strength, therefore never learned how to adapt to or fight an enemy who could meaningfully resist.
A huge part of why FS2 works is because of the expectations set by the Lucifer in 1.
We're expecting to see the crutch again and are pleasantly surprised when we don't.
Instead of cheating by giving the big bad ship an invulnerability flag, effort was put in to make the ship threatening on its own merit.
Yeah the shield stuff is wonky (that said it has an order of magnitude more HP than anything else in FS1 and having the only beam canons in a battle makes a lot of stuff not matter)
I suspect the developer conversation when something like this:
Dev1: How do we make the Lucifer invincible?
Dev2: Give it a crazy strong shielding system!
Dev1: How strong?
Dev2: Like 800,000 shield HP!
Dev1: Cool, unfortunately we don't have time to make a cap-ship shield mesh.
Dev2: Uhh, then just give it 800,000 hull HP!
Dev1: Sure, but that still means players can take out its main cannons
, also the big damage flag doesn't work.
Dev2: Fine whatever, just give it an invulnerability flag.
The primary advantage shields give the Lucifer is immunity to anti-subsystem strikes, without them, it can still be de-fanged.
This also raises the question of why we don't see cap-ship shielding in FS2; even with beams, they provide valuable protection from bombers, we'd have to attack the Saths beams in subspace!
I hypothesis Volition intended to give all ships (from fighters to Destroyers) a shielding system, but had to drop it due to technical issues.