The only concrete thing I've heard for sure is that the unlock system for her weapons is "her commander tells her its okay to use this now" (even with the upgrade that PREVENTS HER FROM BURNING TO DEATH IN LAVA!).
I've heard an unsettling rumor that Samus' first reaction to seeing Riddly in this game (the same Riddly she's pwned every single time before) is to break down crying and to need rescuing by the male marines, but I have not seen anything to back it up or what the context of the scene might be.
Given Team Ninja's misogynistic tendencies, I can't say I'd be surprised if it's all true... disappointed as all hell that Nintendo didn't know better, or keep a tighter grip on the leash, but not surprised.