Well, except that Speaker for the Dead also had Ender as the main protagonist and the events on Lusitania were his way of atoning for what he saw as his failure in Ender's Game.
True, but Ender's also become a very different individual than the child in Ender's Game, and the universe has three-thousand years of change under its belt. He doesn't even appear in the story for quite a while, in which Lusitania thrives with context from the universe without Ender's presence.
The events on Lusitania also aren't purely his way of atoning for his failure, but a secondary benefit to his empathetic answering of Novinha's call for a speaker. They coexist. You could swap Ender out for another speaker seeking atonement for past transgressions, and the story would more or less play out the same way, addressing the same themes. Ender being the original "speaker" just adds more intrigue.
In fact, the very title "Speaker for the Dead" was the pen name he used at the end of Ender's Game when he revealed the truth about the Formics.
Wouldn't be anything wrong with that kind of reference in the next
Mass Effect, either. At that point in the story, it's a millenniums-old label that has taken on a different purpose.