I think part of it is that Mission Breakout was its own separate addition that predated being wrapped into the land so people have a tendency to think of Avengers Campus as just what was built just during the second phase. MB is also visually offensive compared to what was there previously (even though I think the ride experience is superior to that version of Tower of Terror) so even with that there’s an element of “I love the new ride but…”
By the time they’re done Avengers Campus will be the most robust land in the park with two E-tickets, two other rides, entertainment, food and yet I think it’s still going to feel weirdly… off.