First, let me be honest that I love the idea of Epic play, as well as looking forward to second edition.
This of course led me to think about how I would design Epic play for 2.0.
Energy
I think the first thing I would do is revamp the whole energy system. In fact, we seemingly have a mechanic for it right now - charges. If each epic hardpoint had a number of charges, as well as the main body, we can get the mechanic of transfering power - spend (flip) a charge on the main ship and you can ready(flip) a charge on a hard point.
The movement dial
This I would eliminate entirely. Instead, much like armada, give a dial that sets a speed, including a zero speed. You can change speeds as an action perhaps. This speed is the number of charges you spend to to execute a maneuver of that speed. Going fast will thus use up a number of charges that you can't put towards other things.
Damage Deck
I think a single damage deck is probably the way to go. That being said, epic ships should have some more penalizing effects from said deck including loss of...
Crew
I am not talking about the upgrade slot, but something similar to shields - a resource that can be lost. The more crew you have, the more actions or attacks you can take. This may sound like energy, but, it goes along with changing the way epic ships play to a more..
Worker placement
.. type of play style. Epic ships should play different than the fighters and freighters that zoom around. The ship card will be made larger, and have sections to where you can assign the crew. Depending where you assign crew they could be in danger from..
Targeted attacks.
Some areas and points of a ship have always been targeted by daring heroes. Why not take more to cripple a ship, slowly whittling them down to nothing - or maybe killing the crew, leaving the ship as nothing more than a large obstacle.