According to the DMCA notice by EA, "the current audio visual output of the repository creates content that infringes on Electronic Arts copyright."
In an interview with TorrentFreak, creator Nicholas Ochoa said that neither EA or GitHub had contacted him regarding this claim prior to the repository's removal.
"I received notification after the fact from GitHub. Nobody from EA has reached out since and I'm still waiting for GitHub to review my request.
. . .
I just wish they'd have reached out first, I would've gladly removed the content quickly and without issue."
The noticed states that "as long as that continues to happen, no other changes other than removal is sufficient to address the infringement." This shows that the publisher had no interest in having the project fixed, but only removed entirely. This may have been why they did not contact Ochoa with a compromise.
SimCity 2000 is available for purchase on Origin, EA's online game distribution service. This may have been what motivated the DMCA claim, and why which such gusto.
Individuals with passion projects seldom have the ability or funding to go against the legal team of a company like EA. So it's safe to assume we won't see much of OpenSC2K for a while.