Most of the story criticism I've heard fall into a handful of categories:
Overall plot seeming convoluted and hard to follow (which is understandable when you throw both time travel and parallel universes into the same story)
Whitewashed portrayal of racism used for story aesthetics
Ending feeling confusing and/or unsatisfying
Certain story moments feeling out of place and/or undermining things that other story moments set up
I haven't seen much in the way of players expecting/predicting plot twists.