I still think there is no real need to go changing the tables just because a few things in the game seem a little frustrating. Sure, an Aeolus has nearly half the HP of an Orion. The Orion should have more, but keep in mind that the Aeolus has its weaknesses too: it's meant for dealing with enemy fighters, which its reinforced hull and anti-fighter turrets allow it to do. It has two SGreen turrets to deal with capital ships, but the 45-second recharge on the turrets balances it out so that it's not too powerful.
The Orion is a different case. The Orion is designed to jump in, blast away a cruiser or corvette using its fighter/bomber complements as support when things heat up. The ship has several powerful BGreen turrets and several TerSlash as well, which allows it to deliverh heavy damage quickly and effeciently, hopefully crippling the enemy capital ship before it can return fire.
FS2 ships should be looked at in the same light that the fictional Terrans and Vasudans who designed them did. The Deimos concentrates most of its firepower in the forward firing arc with support in its rear. This can mean that the Deimos was designed to get in, do damage on the charge and support itself from the rear and sides while it made its attack. The Sobek, however, is completely different: it's designed for a head-on attack against a capital ship, while it's turrets give it coverage as it dives under a capital ship to avoid the beam turret coverage of say...the Lucifer?
When FREDing big battle sequences, FRED smart. Look at the ships like they're supposed to; use them like they were designed to be used. A Deimos broadsiding a Demon or an Orion charging head-on against a Hecate isn't a smart way to coordinate a ship battle--assume that the ship commander knows something about his vessel. Make an Orion broadside a ship, while a Leviathan or an Aeolus provide some anti-beam cannon fire support and anti-fighter cover. Have the Iceni exploit its speed and maneuverability to keep it out of the firing arcs of bigger opponents, while exploiting its powerful beams to tear apart the adversary.
The tables don't need to be changed at all. They're fine the way they are, and though some of :V: 's decisions may not seem great at times (i.e. Maxim, Hecate turrets), you can trust that they managed to make an enjoyable campaign with entertaining and involving capital ship duels--if they could, so can you.
Hmm... *gets new idea for article relating to FS2 capital ship design philosophy*

*runs off to writes*