I have had fun devising this plan of attack.
I am open to objective criticism and opinion, but every commander is different and depending on your own tactical brain, this may seem tedious or time consuming. Given the nature of the game, i think the later is justified.
Taking out the bunkers, launch pad and Early warning radar helps your fighters to level the base without to much hassle from the ground or air. To do this i prep my marines and send them and my AE to a shuttle. I then send a contingent of prepped marines to the transporter. I prep my fighters and using the same waypoint method SC has devised i get them ready for launch. I deploy the shuttle and fly to a pre-designated waypoint over 20 clicks from the base and fly in real low, in order to stay under search radar. Land about 2 clicks out from the base, designate said targets using the P key, deploy my marines and from the CREW menu and order them to attack designated targets. In order to stop my marines from getting blasted by enemy, I go to the TACOPS screen and transport the waiting marines to a point not for from the C&C building (which seems to be the place from where a majority of the enemy ground forces appear from, and under SAD orders) and watch my transported marines take care of business. I prefer to lead from the front so i usually find myself dying, (i find using cheats to easy and dissatisfying) but you can safely command all your troops from the shuttle. Once your marines have destroyed these objectives, The transporter crew can be EVACed, and the shuttle crew RTB. Give these orders in conjunction with ordering your fighters to launch and RESUME WAYPOINT order. Once they get planetside you can order them to attack any craft or structure using TACOPS or the priority list TAB key in support units mode. Then sit back and watch your your guys attack. For extra firepower in the air, i like to steal any Enemy fighter and help my pilots out. Good hunting.