It would be nice if you could attack with multiple fleets at the same time against a powerful fleet, but then it'd remove the whole point of having fleets. Single fleets only, unfortunately.
With them so much more powerful, killing you in one shot,there's only one way you can fight back.
1) Put nothing on but enough weapons to kill one of their ships in a single shot (everything else is a waste of money and build time)
2) Be the attacker
This will at least give you a 1 for 1 exchange on your ships for theirs, excluding what they take out in their turn.