Continuing from the previous film, the powers that be still go back and forth over whether the snap killed 50% of all life or 50% of all sentient life. Nat seems to imply the former but Steve's observations following the Time Skip suggest the latter.
Steve's wielding of Mjølnir. Was he always worthy and sparing Thor's feelings back in Avengers: Age of Ultron or has he since undergone Character Development to become worthy? Directors says it's the former, the writers say it's the latter.
Steve going back to live in the '40s. Did he create an alternate timeline or did he just sit out of history's way (which means Peggy had to use Exact Words very carefully and Steve turned a willful blind eye to HYDRA's rise)? If it's the latter, then it really messes up Agent Carter, unless of course Steve showed up after the series.
I Knew It!: Many called that time travel would play a role in the film's plot a long time before the first teaser trailer.
There were plans for 2014!Thanos to kill the Avengers of his timeline and present their Cap's severed head to the 2023 Avengers. He would have also beat them back to 2023 and conquered Earth, greeting the Avengers, who'd been a few years late in getting back, atop a throne of skulls.
Thanos was supposed to shatter Cap's shield outright rather than just break chunks off of it.
Based on concept art, Nebula got the Infinity Gauntlet at one point. Whether she was to be the True Final Boss, like in Infinity Gauntlet, or she was going to use it against Thanos, or indeed which Nebula, 2023 or 2014, was supposed to get it is all unclear.
Reunion scenes between Rocket and Groot and Scott and Hope were planned, but ultimately cut.
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