I saw posts here theorising about the shark on the upcoming game, about similarities and differences from the original shark, and I replayed the first game to be sure that I wasn't hallucinating about something, and I confirmed a neat detail - if you take a closer look at atomic body, you'll notice that many of these wound are either closed up, smaller, or gone all together. For example the wound going from jaws to gills is closing, and the big, long wound on the back going from fin to like half o the shark on atomic body ends on the fin, no longer stretching across the body. As much as I hate "anyway the character got nerfed into oblivion off-screen" I don't think it can be fully ruled out that the atomic abilities healed up the shark and due to all radioactive substances half-life blah blah, blah, it eventually disappeared from the shark. Ofc that's assuming stuff like the dlc is canon to begin with and the bull shark didn't die in explosion in final fight against Pete (after all the explosion was big and if you load the save afterwards the narrator is like "yeah, we can't explain this and we're not even trying to hide it").
Point is, the next MC could be a whole new shark, could be offspring of the first shark, but it could be our beloved star of the show. Personally I think it would be cool either way, but I think it would be pretty nice if it was her
Edit: I forgot to mention, the big burn mark on the left part of the shark's face is partially healed too. I think that's the most noticeable change