@ DrathKar,
Hmm, you edited before I could reply, but most of my points stand, so:
Let's put this into a different framework and see if it makes more sense. Have you ever played World of Warcraft or an equivalent rogue-like? We are looking at class issues you would find familiar if you had. The Kol is a defense-oriented warrior (good at absorbing punishment and dealing just enough damage to hold aggro). The Sovas are offense-oriented hunters (good at sniping from a distance and laying traps). The Progenitor is a paladin (heals, buffs, and debuffs) and Marzas would be rogues (strong direct damage and DoT).
Your paladin is going to outlast any number of casting DPS classes in close-combat because his skills are aimed at healing, mitigating direct damage from enemies, and buffing direct damage from his allies. That's what he does, it's how his skillset is designed. He doesn't deal alot of damage himself, but he doesn't need to, because he can keep healing himself.
So if you send two hunters into melee with a paladin you are going to get beaten, regardless of how much damage they are dealing. The paladin is healing himself and the hunters are not. If your hunters kited the pally like they were designed to, keeping out of close-comabt range, then eventually they would win because the pally has neglible long-distance attacks. If you don't like sniping then you could replace one of your hunters with any of the alternatives suggested above, who would either be able to debuff the paladin (Dunov EMP), stun him (Akkan Ion Bolt), or deliver more damage than he can mitigate (Marza DoT).
It's entirely possible the warrior (Kol) would lose to the hunters if they kited properly, because again the warrior can absorb alot of damage but it can't heal itself and it also has negligible long-range attacks.
And yes the Progenitor is a great support cap, with three useful abilities. That's why you see it so often with Advent play. As emphasized above though, its function is support. Against *effective* attacks it's pretty helpless solo, no matter the level. I'd 1 v 1 a Progenitor with an equivalent-level Marza any time. It isn't overpowered and other caps, with a few exceptions, aren't underpowered. They are all *differently* powered, because they all belong in different classes. If your two Akkans lost to one Progenitor, or your two Sovas lost to one Halcyon, then maybe you would have a point.
I'm not really sure what your build orders prove, weren't we looking at capship vs. capships in isolation?
I'm not trying to get you riled up by debating, it's just that you have to consider every aspect of play before you claim something is unbalanced. You have some really good pointers in this thread for countering lone Progenitors Shield Restoration in future matchups, I suggest you try some of them.