They had a personal shield? I never noticed
That being said, we usually wait until the timer runs out and start building game enders when our bases are less threatened
We've never been able to destroy the support bases before the endgame so I can't tell if Yolo bosses are a threat ; by the time they pop, we have dozens of Broadswords waiting for them. Maybe instead you could try making an airdrop wave, with a few Dropinentals landing near the players' bases (not in the bases, I feel that'd be unfair, unless you really want to make it difficult). You could have maybe ten of them transporting T3 units, and two or three with T4. Just an example, ofc
btw, you ever thought about adding vocal messages during the mission? 5iver Survival did it and it was kinda nice
just need to have HQ or anyone sending relevant voicelines when something important happens, like HQ saying "scratch one of the bases" if you destroy a support base.