I need to begin by saying I did not care for the OMAC plotline. At the time, I thought it had a lot of potential, but I did not care for the direction it took in the long run. Between the violation of the former JLI, the absurd self-righteousness of Superman and Batman through the whole debacle, and the single-minded fanaticism of Brother Eye, it just did not work for me at all.
That said, the Infinite Crisis stuff did fold into the story Rucka was telling much more organically than it did in many other titles at the time. You could argue that it was because he was one of the architects of the crossover, but that would ignore how badly his concurrent Superman run suffered. I do not know how much Rucka's vision changed with the development of The OMAC Project and Infinite Crisis and whatever the plans for Wonder Woman editorial were hatching, but I do feel that the storyline evolved, especially after the Medusa arc. The Veronica Cale arc was left hanging; it is unlike Rucka to simply drop a plotline . (Cale got a new job in 52, but her abrupt abandonment in the pages of Wonder Woman implied that she had more to do but there just weren't enough pages.)
The plot: Brother Eye is pissed that Wonder Woman killed Max Lord (with cause), so it broadcast the killing without context to everyone with a screen to help discredit her. Wonder Woman surrenders herself to the Hague to clear this mess up legally. Cheetah attacks, for some reason. Then thousands of OMACs invade Themiscira and Wonder Woman breaks her house arrest to help the Amazons. Faced with a choice between eternal warfare with the patriarch's world and death at the hands of the OMACs, the Amazons petition their patron gods to remove Themiscira from the Earthly plane. Wonder Woman stays behind. Then the Greek Gods themselves withdraw from the Earthly plane. Wonder Woman then gathers the remaining embassy team and dissolves them with a group hug and a generous severance package, and flies off, telling the people outside that she will never abandon them. That would have been a great bittersweet ending, but there was one more chapter that served as a coda, visiting the relationship between Superman and Wonder Woman throughout their respective careers, which was fine.
The best thing about Rucka's Wonder Woman was that Diana stayed true throughout the whole thing. She embodies the best of her people in the same way that Superman embodies the best of "our" people. She is steadfast and caring and will do what she thinks is right regardless of what anyone thinks about her, whether it is Superman, Batman or her own patron goddess Athena. While she is a warrior, she is more importantly a teacher and an inspiration, and Rucka got that in a way that not everyone does. And THAT is why I gave his entire run 5 stars despite having quibbles with certain plot points or character beats.