The single biggest killer of my ships in battles is loss of fleet cohesion. Individual ships can easily become isolated and overwhelmed, while escort orders can result in the escort ships either putting themselves in too much danger, or not contributing to their escort target's survivability at all.
What could help resolve this is Squadrons - these would be set up in the campaign layer. Once in battle, ships that are part of a squadron will stick together, attempting to maintain a given distance between one another. They'd attack the same target wherever possible, while any orders given (except retreat) would be given to the whole squadron by default. They would decide to withdraw simultaneously when appropriate, instead of the escorts often putting themselves between the enemy and target ships, which is usually much more dangerous than necessary. Full assault would not be mutually exclusive with the squadron acting as such, in the same way escort orders are thrown out the window.