I don't know if the Chozo will be factoring in very much with this particular game, since most of what they've shown is from urban settings, possibly within Federation territory. Her years growing up amongst the Chozo defined her role as defender of the galaxy and placed her destiny in opposition to the Space Pirates and numerous other evils...
But then again, there's also the murky period between her graduation from Chozo training and becoming the Federation bounty hunter we know and play. There's a lot to be mined here, and from what I've seen so far, I'm willing to accept some intrusive story as long as we get those awesome action sequences up our collective wazoo.
Look, it could be worse, it could be MGS4 the 80-hour-long cutscene.
I don't think we have to worry about Zero Dignity Samus, considering Itagaki isn't running Team Ninja.
I'll be honest, I've always seen Samus as a cold, proud, admirable warrior goddess with little concern for mortal affairs; this is mostly due to a lack of characterization (and perhaps a desire to separate her from her feminine contemporaries). The ramifications of Fusion and Other M are quite alarming to me, but I can see what the designer's getting at in making Samus more approachable; rather than simply being a faceless cipher or idol, she can empirically represent a story or identity.
There's more to her than we could have ever imagined when we first blew into that NES cartridge; Samus is growing up, and if you really love her, if you want to hold on to her, you will have to get to know her. Maybe your relationship with her will change, maybe it won't, but one thing is for certain: the official site's piano theme tugs my heartstrings.