Black Widow: No Merchandise
You win the thread, obviously.
( Here, the core theme is simpler: "Do you think you've seen the Black Widow angry? No, you have not." )
That's pretty frikking awesome.
I would model it on The Bourne Trilogy with the villains being the project that created her.
This seems simplest, and cleanest, I'd also think along these lines.
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I also dislike the immortal Natasha, and I'd eschew it here. It doesn't help make her character better, but actually devalues her incredible skills, and also makes it really weird that a spy with 70 years of experience still plays third fiddle to spy with 30 years of experience like Nick Fury.
Black Widow
Basically, the first movie would be a dive back into the Red Room, really exploring what that is as a KGB throwback, and a lot of the film would revolve around The Winter Guard, who would be almost obvious pastiches of the Avengers. Red Guardian is Captain America. Crimson Dynamo is Iron Man. Ursa Major is Hulk/Thor-ish. Darkstar is Scarlet Witch-ish. As a whole, her break away from the Winter Guard, as told through flashbacks would be used to push the story theme of her being a separate entity from the rest of the Avengers, even though, up to this point, she has been largely framed as an Avengers supporting character. Her defeat of the Winter Guard as a whole will cement and resolve precisely what her contribution to the Avengers is and why she's 'on their level' sans powers. Essentially, Black Widow as 'the Batman' of the team, as opposed to Hawkeye 'the heart' and Cap being the paragon archetype.
In addition to this, each member is a different aspect of her story, Red Guardian is her ex-husband, and the current head of the Red Room, so there's lots of history and emotional drama there. Darkstar, the young girl with Darkforce Powers, can act as the locus for Natasha's maternity, so to speak. Not that it's necessary, but when I look at Rue and Katniss, or Newt and Ripley or John and Sarah Connor, it's an angle that works for the best and most successful female character, and here, with the object of her protection, the girl she's trying to save from the Red Room being her enemy, it makes the twists that much more delicious, that she also works as a dark mirror, or reminder of Natasha's past. Crimson Dynamo plays a sort of old uncle reluctant villain role while Ursa Major is more for comic relief.
The whole thing would play out in spy themes: a little Bourne, a little Bond, a little Mission Impossible. Widow showing that she's so clever by holding onto a plot reveal until the climax of the film. Criss cross the globe ever so slightly, let us show off her being undercover, infiltrating places with nothing but a shoe string and a can of soda. Supporting cast limited, would love to see Hawkeye, Winter Soldier, Daredevil, Rick Jones or Bruce Banner. She basically just needs a male confidant, someone who seems like they can help her, but in actuality very much needs her help.
Black Widow vs Black Widow
A plot that goes to the heart of Natasha's new life played out by Yelena Belova, the new Black Widow. She serves, clearly, as a dark mirror to Natasha about what kind of spy she was supposed to be, at was at one time. She is capable of taking apart the entire Marvel Universe, and Natasha is the only one with the wits and knowledge to stop her. Belova also employs something cool and very Marvel-ous like the Super Adaptoid, bringing another BW vs Avengers type deal, except this time, she can't win, and she finds a way to lose in a way that gets her what she wants. So, more like what happened in the JLU cartoon with Amazo if you can recall those days. Watching Natasha's personal life crumble and how she reacts to that, perhaps interspersed with flashbacks of her old life crumbling brings the character to the roots of what she is, this survivor, by any means necessary. While the first movie was designed to make us what vengeance with her, this movie is more designed to make us want her to be safe and happy as we see what little she has torn away and then watch Belova kick her while she's down. We watch Natasha survive anyway and get the keen sense that she can make it through pretty much anything, and when she comes back, she's going to be wrecking shop..
Black Widow: Nefarious
I feel like someone needs to be doing Count Nefaria, and I feel like Black Widow is as good a place to start as any, with Nefaria leading the Zodiac and the Maggie and Black Widow infiltrating all that, becoming close to Nefaria only to be found out and things going haywire from there, with lots of betrayal and intrigue and really f'ed up relationships everywhere you look. That's where we'd cement that Natasha really is that smart enough to coast through impossible situations on the skin of her teeth, and that she really does want a simpler happier life that she believes she can't have. Perhaps stuff we already knew, but we wind these things into a satisfying conclusion, not unlike what Iron Man 3 did with Tony's "You know Who I am" "I am Iron Man" refrains.