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There is a long journey for Jacob and MIB between Across the Seas and Ab Aeterno. I will attempt to convey my thoughts on their motivations and the time they spent on the island. My theory is based on one major point and that is that, MIB did not intend to become mortal again. He does not hate being the smoke monster he simply hates being on the island, and wanted to leave with his powers intact.
I belive that shortly after the events of Across the Sea, MIB appeared to Jacob and revealed his new powers, though I suspect at this point neither of them fully understood what had happened. MIB searches the island for the source, but Jacob keeps it hidden which leads to a confrontation. Jacob admits that he doesn't think MIB should be allowed into the world with his new powers as he would invariably force everyone to do his bidding and destroy anything and anyone who got in his way. MIB has lived with people for 30 years and firmly belives in the inherent evilness of man, people are weak, greedy and corruptible by nature why shouldn't he rule them as a more powerful being. Jacob states his point that people can be good even in trying circumstances and he will prove it, and that he will never allow MIB to leave and destroy the world. Jacob then begins bringing people to the island and I belive that the French Team are a perfect example of what happened to all the many people brought by Jacob before the Black Rock. They arrive on the island and are slowly corrupted by MIB until they eventually kill each other.
That's my thinking of the dynamic between Jacob and the Man in Black int the 1800 years which we have no knowledge of. I have tried to make a few assumptions as possible while still explaining things such as the nature of their debate and all the talk of the world ending if MIB gets off the island.