I assume you've already figured out that your first three tasks are 1) target an engineering pod at Flak Drone 1, 2) target an assault transport at Bunker Station 1, and 3) warp to the two Cantharan assault transports and take them out personally (you can build a gunship and a cruiser to help, but don't wait for them). You can neutralize Bunker Station 1 before the assault transport arrives, and if you stretch yourself thin, you might be able to proceed quickly and take Bunker Station 2.
The important thing is that, by the time the cargo ships start arriving, the front line should be between Bunker Station 2 and Flak Drone 2. You should be applying pressure forwards, even if you only managed to neutralize Bunker Station 2 and not take it. I don't generally find I need to divert defenses to the shipping line in this situation.
Other notes:
You don't need the Battleship to win, it's just helpful. You can ignore it and still do OK by focusing entirely on the bunker stations for their resources.
Assault transports are good combat ships, other than their lack of warp. They're good to have on guard duty for bunker stations or flak drones once they've spent their two EVAT payloads.
This was always my favourite level.
Here's my standard starting tactic:
1. Send an engineer pod to flak drone 1
2. Warp out to a position just to the left of Bunker Stn out of range of its weapons 1 and hold position. This is Assembly Point A. The Cantharians will attack Bunker Stn 1 and usually neutralise it.
3. Build a gunship and add it to your cruiser.
4. Build an assault transport and target it to flak drone 1 (which will be yours by the time the assault transport arrives)
5. I transfer my control to the Gunship and then build cruisers to add to my fleet.
6. Kill any engineer pod that moves in on your flak drone
Generally the two Cantharian assault transports die before they can capture the bunker station. So you can ignore them. When they do die the Cantharian carrier leaves after the station is neutralised.
6. Move in and take control of the space about the bunker station and order your Assault Transport to capture it.
You have now secured the area.
Watch out for a steady stream of Cantharian engineer pods heading for your flak drone.
7. Occasionally the Cantharians will capture station 1 in which case you must move in and kill it immediately with the gunship.
7b. Sometimes the Cantharian carrier hangs around. You will have to kill that also.
8. If you take and hold bunker stn 1 the transports will enter the system and build the Battleship unmolested.
Then make it up as you go along 
9. Once you have taken Bunker 1 it is best to dig in and defend until all the transports have arrived even if the Cantharians take Station 2, though if you are good at strafing Bunker Stns with gunships you could have a go at knocking it out.
Sometimes if I do well, I can grab the second bunker station, though I usually go for the second flak drone by building a second engineer pod and positioning it at Assembly Point A until there is a chance to sneak it in against the flak drone.
As Pallas said, you don't need the Battleship to win. First time I played the level I didn't get it and had to dig in and win the hard way. My, that way a long time ago 
hope this helps
You can see me playing through this level at http://youtu.be/PSa3EwEuh6A.
I wouldn't say it's a particularly good playthrough on my part, but it shows my strategy in general. Note that I differ from LCA in that I immediately go for the Cantharan Assault Transports—better safe than sorry, I feel. I'm pretty aggressive about taking both bunker stations, but if I lose one (as I did) I don't feel it's necessary to retake it.
One technique I demonstrate (arguably an unfair one…) is manually using an Assault Transport to take a bunker station which has not yet been neutralized. EVATs trigger when a computer-piloted (or autopiloted) ASLTTRAN is in range of a bunker station it's targeted to. When a computer is ordered to a bunker station, it will launch the EVATs at range, which won't succeed against a hostile bunker. However, if you personally fly an ASLTTRAN directly over it, and trigger autopilot, the EVATs will be deployed directly, and you'll immediately take the station. That's how I took the first one at 2:46 in that video.
