I could be wrong, but even before Uncle Jun's legal problems, I thought it was agreed between Jun and Tony that to save face for Uncle Jun...Junior would be the "face boss" and officially titled boss of the family, while Tony was the real boss in the background.

I think Jackie Aprile wanted Tony to succeed him or perhaps the DiMeo Don in prison wanted that also.

Well not everyone liked the way Uncle Jun was running things anyway.

-A Streetcar Named Desire-

Stanley: You want a shot? (offers liquor)
Blanche: No, I rarely touch it.
Stanley: There's some people that rarely touch it, but it touches them often.