Three Frigates OR One Escort OR One Science Ship OR One Cruiser.
The Science ship always starts with feedback pulse.
The Cruiser always starts with a defensive screen that makes it immune to damage for about 15 seconds.
This is getting old. Maybe we could make the Random fights a little more random?
Science ships and Cruisers use a few more abilities.
Have the next attack wave arrive BEFORE the first is destroyed. You could rig it so when the first ship is at 75% hull there is a small chance the next ship arrives. A larger chance of reinforcements at 50%, Larger still at 25%. You get the idea.
Mix up the deployments. Cruiser with 2 frigates. A Pair of Escorts. A Cruiser and a Science ship.
Along with multiple ship encounters you can vary the enemy strength, Enemy -1 level or +2 levels.
Making the progression of the battle a little less predictable might be nice.
When multiple number of players are in one of those missions, the game engine does mix and match. I have faced two science ships with two frigates when three of us entered an area.
As for the 75%, I have fought some ships get the drop on me and when I reduced them to 10%, they managed to finish me off. As soon as my ship's warp core explodes, the ship's hull is fully healed, and only its shields are weakened. If the ship is on the far side of the instance, the shields are usually fully recharged by the time I return. I would support having more ships war in, on the contidion that this auto-heal function was simultaniously disabled.