My feeling about the Atlantean origin thing was that it took her from the Superman Family, and put her into the Aquaman Family. But only very, very loosely. It was a trade down IMO. But it may have saved her from the ax, if only until they basically offed her for the next decade and change after Flushpoint. It had certain narrative bits that could have been used to tie her sort of to Dr. Fate, and had it been done at the time it could have been an excuse to expand and diversify DC's magic line-up, but they didn't. And they never really did anything with her and the Atlantis thing either, at least nothing I want to remember. But honestly, had you not known she was Atlantean during that time, you could read those stories and think she was still Kryptonian, just being a bit shy about using the flashy vision and hearing powers. Or she forgot about them as such characters frequently do when the story requires them to, so it isn't like they built some big, worthwhile thing with her.
The costumes, some of them, were fine as such things go, not the editorial designed "P" costume of the early nu52, (literally, according to Kevin Maguire IIRC, though I think Perez, (RIP), also had some comments that suggested that editorial also interfered with the story, and Maguire IIRC mentioned having to redo art because they'd wanted something different close to deadline.
When was this big return of a mostly JSA team supposed to happen, and where did Dr. Fate get his costume?