(Of course, I don't expect an answer, but ...)
Is there a plot-driven reason that Michael wasn't a part of X or at the church?
I can't think of one. All I can come up with is that the kid who played Walt was "too big" to film any scenes that would be believable as 2004. That's a copout, though. They could easily have filmed Michael and referenced Walt off-screen.
All I'm left with is:
1) something personal between TPTB and the actor himself
2) bias from TPTB that somehow rated Michael's character as "minor" -- (complete B.S; Artz, Ana Lucia, Charlotte get shoutouts but Michael doesn't?)
[Even Jimmy Kimmel made reference to why Michael wasn't around and Harold Perrineaux gave some cryptic shrug and smile.]