I like your overall ideas in regards to the Eradicator, but I don't like "it" as a woman if he is going to provide a physical conflict to Superman. If the Eradicator acted as a guide to Superman to replace Jorel then I am all for using a woman character.
Yep, we're talking about it being a mothering figure at first to replace Jor-El. However, towards the end, becoming more agressive and violent. Having a woman be this just resonates on so many levels whether it be for providing a romantic rival for Lois Lane (not overly, but just enough), a Kryptonian mother figure for Jason, and also to contrast what I'd also have in my treatment: Luthor, Donovan, and Metallo.
Also, while I'd leave the fist-fighting to Metallo and Superman, I would probably have a singular confrontation, final confrontation, between The Eradicator and Superman, probably more of a chase, with Superman holding back his blows because he sees her as a woman, but ultimatly taking care of her by driving into her, pushing out through the atmosphere, driving through space, through asteroids towards the blazing sun which he barrels into while dragging her with him.
The Eradicator could play on the whole idea of what is the role of Superman, to what extent is too much? What are the lines of his power, when is he interfering? You could also play with the tension of Superman being a father now and being more intimately connected with Earth than ever before...so does Jor-El's warning still ring true? Doesn't a parent have an obligation to do all in their parent to create a better world for their children? With Jason, Superman has found a new moral imperative? Is he justified now in intervening in wars, defusing nucler annihilation, solving terrorism, world hunger, etc.? The Eradicator could come as an individaul to say that he's failed...countering this with Luthor and Donnovan trying to recreate a Superman, bastardizing the Gods, false idols, using the kryptonite shard with Superman's DNA on it.
Donnovan could work for a government agency that was trying to buffer the affects of Superman's absence. He can be a well-refined, yet fanatical believer -- and phobe -- of aliens, feeling that Superman is more dangerous than heroic. His first development is Metallo, a cyborg in the strictest sense of the word -- no liquid metal, no nanobots, we're talking a cyborg that by the film's end with find Kryptonite as his inexhaustible life source (metallo would be struggling with his own mechanical survival.) John Corbin, i.e. Metallo, was a family man whose family died wile they were on vacation, their train derailing. Corbin was near death but was rescued by Donnovan, who rebuilt him.
Donnovan's team is closely watching New Krypton, and also, he travels to Morroco and unearths Lex Luthor, offering amensty for his crimes, a huge sum of money, and a large plot of land outside Metropolis should he help him (he works for the gov't afterall) -- Luthor has the only remaining shard of kryptonite that is also laced with Superman's DNA. Luthor could manipulate Donnovan and gain the access he needs, stealing Metallo away from Donovan by playing on Metallo's hatred for Superman since he blames Superman for his family's death. Luthor plays on Metallo replacing Superman, something that Donovan stops short of doing. In the end, Luthor could also reveal to Donovan that his genetic experients in recreating a Superman for the gov't can be solved if he examines Jason, Superman's son. This can lead Donovan to Jason, a sort of X2, mansion scene where Richard had to protect Jason from being abducted and fails -- (think of a great moment that, Richard is already aware that Jason is not his, he and Superman have discussed it and superman has said that Jason must never know and must grow up as a child of Earth before becoming a man of Krypton. So, Richard is distraught but nevertheless, fights to his near-death to protect Jason and in the process, as Jason is yanked from the car or what not, he screams, "Daddy!" -- just a moment there) -- anyway...
This could be tied in with the Eradicator being disgusted with humanity, and now that she sees the bastardized blood being reproducesd, sets to taking out Donovan and crew. Superman is of cousre all caught up in the middle of this -- how? haven't htought of it...I tend to pin down what the actual villianous situation is first before figuring out what and how the hero will fit into it properly.
You could have the finale take place in the Fortress of Solitude, where as i said, Vrill Dox under the guidance of The Eradicator, is reversing Kryptonite to eradicate the entire Earth and prepare it for repopulation by Kryptonian survivors, should they find any or something.
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