Your base attacking plan seems to assume the Gundams can just ignore physical damage and fly through anything undisturbed. But if that was the case why attack the base at all, they could have just flown away from the start ignoring the large number of artillery shells raining down on them and the dozens of mobile suits trying to grab them.

Unfortunately, Anno Domini Gundams are susceptible to physical damage and momentum transfer so if they had just tried to fly through the bombardment they would have been knocked around repeatedly and that would have created openings for them to get grabbed by the ground forces, which they'd then have to repel before trying to escape again with the exact same results. I suspect that's exactly what they did for all those hours:
1) try to run,
2) get forced to take cover thanks to artillery,
3) get harried by a mobile suit squad for a while,
4) destroy/repel that squad,
5) back to 1.

It's like fighting a pack of wolves, they surround you and just keep attacking your weak points trying to wear you down until you can't do anything anymore.
Each time they would have gotten more tired, more prone to making a mistake, and from as time went on the skill level of the opponents would have probably been getting higher. A potentially viable solution would have been trying to escape upwards, I don't think the Gundams can make orbit but they could potentially have a ceiling higher than the Flags/Enacts, however flying up would still subject them to bombardment for a while which could affect their ascent.