Don't ever think that the paragon can stand toe to toe with the Onslaught... you'll just get slaughtered by the autocannons and then the H assault guns. If you want to try it, try it with 4 tachyon lances. You might survive
What! This is total nonsense. I recently captured a paragon and I switched immediately to it as my flagship. The paragon is absolutely insane with max vents, flux conduit, hardened shields, and stabilized shields. You'll have to sacrifice 4-6 weapon slots to get this though.
I've been able to kill TWO enemy onslaughts and their fighter wing escorts with my paragon this way. A note though, its best to only fight one onslaught at a time, by keeping one between the other's line of fire. I'm pretty sure nothing in the game can withstand a flanking attack by two onslaughts at the same time if a paragon can't do it.
It's the reliance on shields and the non human element in the AI (not properly understanding that the Onslaught can be kited easily) if you tried that same setup with the paragon as an AI against the onslaught I highly doubt it would survive. Also, a Dominator has a better chance than a paragon (paragon relies on shielding a large portion of the time to survive) as it is pretty heavily armoured (the beauty of armour is that while it cannot heal, it's more usable than shields as it's almost always up, although if destroyed it's gone for good until after battle).
Also, what weapons? If you get rid of 4-6 weapon slots (I'm guessing small slots) then you're in a lot of trouble if you get attacked by anything more than a few ships as those extra missiles and fighters run circle around your ship as it's incapable of fighting multiple threats.
It's weird, I kind of have the opposite view with regards to reliance on shields. I prefer when ships rely on shields because they're quicker and cheaper to repair and shields are effectively infinite. It's a subjective thing mostly, but the Paragon's shields are redonkulus, especially with a veteran or elite crew.
Also, leaving off weapons is a perfectly valid tactic- it frees up OP to either add on more vents or capacitors, or put stronger or more useful weapons in the remaining slots. Slots with awkward, purely defensive, or useless weapon arcs are good candidates for ignoring. It really helps specialize a ship, or better gear it towards its strengths. If you find you never use the missiles on an enforcer, for example, you could get more capacitors for it instead.
Also, you're right that the AI with that setup probably wouldn't beat two Onslaughts, but that's mostly because the AI wouldn't use the same tactics. It probably wouldn't matter what setup the Paragon has in that situation.