Yeah - they should've made more use of Sue as a SHIELD Agent. One issue of SHIELD and few issues in the Time Runs Out arc at the end of Hickman's Avengers run - I wish they'd brought in that twist for her earlier. She could come back, rejoin SHIELD, and get a solo book. The Future Foundation would return as well, but would no longer be run by the Fantastic Four. As mentioned, Spider-Man could take over that, as he already has the Baxter Building. Could get Scott Lang involved too - he'll be needing a new job after the events of the last few issues of his cancelled solo book. The only ones needed for rebuilding the multiverse were Reed, Franklin, and Molecule Man.
As for Ben, maybe he could join the Uncanny Avengers, where Johnny already is. Or form a new Defenders team?