Wave 5 gets everyone, and I think part of the problem is ships coming in from 8 different directions. But they're all in a plane - I wonder, if you had 5 ships all with tractor repulsors, and spaced them evenly around the transport, could you keep the enemy vessels from getting within 10km of the transport? I wonder if this has been tried.
I always play Pug, so my game is usually rather unorganized!
The only way to beat this is to bed a naive young Orion Starfleet cadet working behind the scenes of the simulator and convince her to wait until you're playing to open an e-mail you've sent her with a virus attached that's designed to nerf the enemy ships.