"Outlasting" doesn't work very well when you are facing overwhelming force. You need burst in that case. Kill something quickly using all your flux (or as much as you can/need to), active vent, and kill the next thing.
The AI cannot do this! Once they use up flux bursting, AI battleship just sits there and let the surviving enemies strip armor and grind away hull. I tried burst loadouts for AI Paragon. AI Paragon simply dies several seconds later than Onslaught or Conquest. Dying seconds later than a 40 DP capital does not make Paragon worth 60 DP.
For the player, sure, burst loadout works. But, two plasma loadout with monstrously high capacity and dissipation is surprisingly effective. Good enough to compete with a burst loadout in general effectiveness.
@ Goumindong: I guess he uses HAC because that is 10 more OP for capacitors, and it appears part of the loadout's effectiveness is sheer flux capacity to absorb hits longer.
I tried four autopulse. AI misuses it and dies quickly enough (at least not if some OP is used for campaign stuff). Great alpha burst in player hands, though.
That's where the other ships in your fleet come in. You need something fast and tanky to take the heat off the paragon after it blows its load. AI Odysseys are perfect for this I find, but it could also be a player role with something like an aurora. But anyway, you are never going to win on sustain vs a superior force.
Played Paragon some more against Ordos and SIMs.
The weakness of two plasma Paragon is finishing stuff. More than once, my fleet of two plasma Paragons had to corner Radiants before finishing them off. Also, killing speed of two plasma Paragon in SIMs is good, but not optimal. The slower killing speed means Paragons' PPT often times out in double Ordos fights, and I still lose one or two Paragons in double Ordos with Radiants. Two plasma Paragon really needs near max capacitors or it is no better than the some of the more conventional loadouts.
I tried four lance, two lance/plasma, and four autopulse without the campaign mods. Four lancers with high capacitors are great for mop-up duty or as a player-piloted sniper. AI has problems in fights when lance crossfire is not enough to overcome shields. Two lance/plasma with near max capacitors seemed more efficient than two plasma Paragon. I can finish double Ordos fights without PPT timeout. The AI ran a bit hotter, but that was compensated by lances picking off approaching targets and finishing off enemies weakened by plasma. As a playership, it can almost solo the simulator. (It probably can, if I can pilot it better and/or respec my campaign skills for more combat skills.) Two lance/plasma needs high capacitors, which means no campaign mods (at least for AI). Four autopulse… four or five Paragons firing the whole clip at the same time slows my computer like Spark Drover spam. Firing whole clip can be dangerous for flux bar. Did not seem to perform any better than other loadouts. It is usable, just... not my first choice.
I guess AI Paragon with some loadouts that are totally optimized for combat are worth 60 OP. It does not have the OP to spare for campaign luxuries, despite appearing to have lots of OP.
Do not use those hullmodes, it is mistake. Lets look, Efficiency Overhaul, you need less use of fuel and supplyes? take more tankers and freighters, you need faster CR recovery? take more ships for replacement. Augmented Engines? I think you want to say Augmented Drive Field? take more tugs. I have just 3 ships for fighting, 2 paragons and one astral (and it is enough to hunt everything), other slots are full of tugs, tankers, freigters, salvage rigs, and it is enough. You can add 3-4 ships for battle, it is no problem. It is some expensive in fuel and supplyes, but there is no problems with that. 
do not be afraid about it. Just hullmodes which are assisting in battle.
I can agree with this for Remnants, provided I have a colony built next door for the purpose of farming them. For nearly anything else, I do not need to optimize this hard to wipe out humans painlessly. Taking more capitals, tankers, and tugs is easier said than done, except at the very end when I have everything and practically won the game. Bringing few capitals, whether battleships or more Prometheus, is already a high cost. Four tugs is significant, and that assumes Navigation 3. (For a long time, I played without Navigation, and I needed four tugs even with Augmented Engines. My fleet bled fuel like crazy. I would not want to bring more capitals and six tugs!) If my fleet travels long distance and does just about anything other than farming Ordos for Sparks and cores, I would like to run a more lean fleet with campaign mods to cut costs more. (This is for unmodded game.)
While I love the Paragon and consider it to be the best ship in the game and better than anything in a majority of mods as well, I do find that multiple Paragons do not synergize well. One paragon is great. Two paragons, regardless of whether one of them is player piloted, do not work nearly as well as a Paragon + other ships. My personal combination is Paragon+Astral+Odyssey, with the astral(s) doing heavy damage bombing runs to pick off targets, the Paragon charging up the middle and occupying the enemy force (while doing considerable shield damage), and the Odyssey(s) running interference by dodging in and out of combat.
What happens with 2 Paragons is they essentially fight two separate battles. The enemy might put token pressure on one while focusing the other, and due to their slow speed there's nothing the un-pressured Paragon can do to help its partner. As a result they simply die alone one at a time. Even with player piloting and specific orders there's little one can do to prevent this, whereas when I run Odysseys + Paragon I don't even need to issue orders at all, it just works out of the gate.
and the mines just blow up after a while. SEEMs legit not very usefull at all even as anit fighter protection.