Chief among potential conflicts is the environmental arena, in which the federal government will be GM’s largest shareholder and the chief regulator of vehicle fuel-efficiency standards…

“The government has conflicting policy objectives now,” says John Casesa, a veteran Wall Street auto analyst who now heads his own advisory firm. Mr. Obama’s new regulations will “cost a lot of money” and “create substantial risk to the government earning a good return on its investment,” he says.

That could force the government to pump more money into a new GM down the road.

“The government will open its pocketbook again to help these companies rather than back off on its environmental agenda,” Mr. Casesa says. “It can’t have it both ways.”