Even though I don't think they should change the ending, it will be fascinating to watch what decisions Bioware makes from here on out. If they do opt for the indoctrination theory then they will have to figure out how to handle the content for those who chose the control/synthesis choice. Because they certainly won't make content that's only available for those who chose a single specific ending choice, they'd make it so it's available to play for everyone who finished the game.