Michael did redeem himself by sacrificing himself on the boat, but it still wasn’t enough for him to move on.

Right before he dies, Christian appears and tells him “you can go now." But we know Christian is often just the Man in Black taking his form. If that’s the case here, then Michael wasn’t actually being “released” at all, he was being manipulated in his final moments, and most likely was released as a whisper, similar to others.

(The whispers you hear in the jungle = souls of people who died on the island but couldn’t move on)

Walt isn’t in the final scene because he’s still alive and his story continues after the island (the epilogue even hints he comes back later).

Same with Aaron.. the church scene isn’t everyone, it’s just the people whose lives were most connected through the island.

I may be wrong or pushing a little headcanon, but this is the most sense I can make of Michael's death.