Well this changes things drastically. If the opponent is throwing TIE Defenders into the battle and you are on equal economic footing you are going to be hurting badly, since they have the same cost as x/a-wings but are much more potent. May be time to base delta zero his systems rather than fight him head on. I dont remember what bombardment strength you need to accomplish that, but I remember it was very high.
My biggest issue is that the empire at this point loads up with all TIE Defenders; and he peels off one group to attack my cap ships; while the Attacking Fighters command specifies one group; which 90% of the time is NOT the one hitting my cap ships
You said "he peels off", are you playing against a human?
In either event the issue is you are facing an end game multi-role fighter that can be stacked for serious damage. You just need to punch through the numbers faster, and your best bet for that is stacking your fleet with X-wings. They are the better rebel superiority fighter owing to their higher damage. Mixing in a few A-wings can help the X-wings live longer, but the X-wings have half again as much firepower so make those the mainstay. Trying to reactively use the escort command to send your fighters around to ships under attack you are going to always be playing catch up.
Are you using the stand off or surround commands on your gunships?
If the losses are hurting you that badly, you may need to switch things up and send cheaper, expendable fleets of gunships and escort carriers loaded with X-wing and A-wing escorts. 4/2 or 5/1.