It does seem rather convoluted to just get her out of the way. And what was with her unknowingly building a bomb despite all of it? I really hope there's an amazing conclusion that brings it all together, 'cause I've definitely been hooked by the story the first three issues, and I'm absolutely in love with the art, but this issue has made me extra nervous about how it's all going to wrap up.
I don't agree James should have been Bucky, though, or anyone we know. This is Natasha's story, and adding another brainwashed big name character in there instantly takes away from that. Personally I think it needed to be someone we would question and be suspicious about in the beginning, that's what grabbed me and had me theorizing, and James fit that bill, but at the same time it made this issue not work for me. IMO it was this issue that was the problem, not the initial setup.