Shailene is no longer playing Mary Jane in Amazing Spider-Man 2 nor any of the future films.
The
assumed reasoning being that
A) Her inevitable schedule for the Divergent sequel will interfere with ASM3 and 4, creating a risk in her availability for the sequels.
B) They decided to remove Mary Jane to streamline the story as well as go a different direction. That direction being......
Sarah Gadon of "Cosmopolis" fame.
It seems that, in a preemptive strike, Webb and Sony casted the role of MJ in ASM3 (where she will now make her debut) VERY early to avoid a similar fate that Shailene ultimately suffered.
All of this has (except the exact reasoning for Shailene's complete departure) been confirmed via reports in the last 24 hours.
Gadon herself confirmed her involvement in the "ASM franchise" earlier today, despite a tweet earlier saying the reports of her casting being false.