<<And altering the entire ending during production simply to setup the Matrix Online, ruining whatever proper ending we were meant to get originally.>>
Hunh? I never heard this before.
I was a member of TheLastFreeCity forums back in the day, during 2003 after Reloaded's release links were posted about production delays, alterations that had gone on during the 2000-2003 period to do with Revolutions ending.
When the Matrix Online was announced as a follow up, before or at the time of Revolutions hitting cinemas, I remember there being remarks to the effect they had filmed only some bare scenes of an orignal ending, but changed it mid-production to allow an "open ending" to continue the story.
There was no solid evidence for it back in the day either, but no one really doubted the W's where either dumb enough, or greedy enough to have done so.
Either way, Revolutions was a clusterfuck on and off screen. If the series ever is rebooted, please don't let anyone involved with the originals come back.