EMP does not work on Combat 10 flagships; they usually shrug it off, and even if EMP knocks-out something, it is repaired quickly. Their engines are very hard to impossible to take out thanks to max Evasive Maneuvers (-80% damage to engines, or something).
Paragon is tier 1. Piloted by the player, it can destroy the entire simulation fleet, deployed as much and fast as possible, singlehandedly. It is hard, and it needs Hardened Subsystems to have enough time to fight before losing too much CR. Onslaught lacks the defenses to do it. Other (standard) ships lack defenses, firepower, and/or peak performance.
Onslaught probably can focus-fire more guns than Paragon, but its defenses are nowhere as good, meaning it is easier to take out. (Player does not need to work as hard to destroy a skilled Onslaught, but the player probably cannot tank everything with his skilled Onslaught from an entire simulator fleet.) Also, AI Onslaught can use its Burn Drive stupidly, possibly giving you an opening. That said, Wyvern is right: one mistake against a Combat 10 Onslaught and you are either severely mauled or dead.
The reason enemy Combat 10 Paragon flagship is dangerous:
* If you need to get within weapons range to attack (because you pilot high-tech ship like Medusa or something else with poor shot range), you are dead fast unless you are Hyperion or a big battleship of your own. Needlers, Heavy Blasters, Autopulse Lasers, and beams all coming at your ship will pile a whole lot of damage very quickly.
* Fortress shield lets it tank very well. The only way to bypass it reliably is Hyperion teleport cheese. If you cannot get around the shield, you can pound on it a long time. Meanwhile, it may be regenerating hull as it chills out in its bubble. It is a royal pain to take out.