Both companies commit the same crime, the nature of which is unimportant.
It takes 30+ years for the case to enter the judicial system. In the meantime, the guy running the first company is still there, while the 10 employees of the second company are no longer the original 10.
Is it as fair to prosecute the second one as the first one? I don't think so, because at that point you're assigning way too much value to the legal fiction of personhood. A company is made up of people, and I really don't see how there is any justice to be served in prosecuting people who didn't actually commit any crimes just because they work at a place with a certain name.
The company must maintain the liabilities of its history. If a refining company dumped waste directly into the ground, then 30+ years later it should still be held responsible for clean up, even if all of the people involved have retired. Otherwise, who is responsible for the cleanup?
Or, suppose that we find that Disney had illegally acquired the copyrights and trademarks to Mickey Mouse from Person X. All of the people involved are long dead, though the inheritors of the estate of Person X were successful in their lawsuit. Under your view, it seems that the inheritors could not sue Disney because none of the people now at Disney committed the original crime. That's an absurd conclusion.
You seem to think only one of these exists.
Most significantly, going forward, corporations will weigh the potential costs of litigation against the profit of doing business with regimes committing crimes against humanity. Which is what we want.
a company will have almost entirely changed in 30 years - the son should not have to pay for the sins of the father, etc.
If the company signed a 100-year lease 30 years ago, should it no longer have to honor it?
If the company agreed to pay pensions to its employees 30 years ago, should it get to stop paying them?
If the CEO of Chrysler retires, can I stop paying the loan on my car?
The point of a corporation is that it's a durable entity (NOT a person, but a person is a good analogy much of the time). That's why corporations can own property, be insured, get loans from the bank, and otherwise enter into contracts -- because there will be an entity there tomorrow that will be accountable for those transactions -- regardless of who owns its shares or who is on the payroll.