The best thing about "Lost" is how well misdirection is applied. The writers don't pull a fast one on the audience; they simply present information in such a way that the truth is right there in plain view, but it becomes difficult to see past the red herrings. In this case, many had pointed out the evidence that something unusual was going on with Locke, yet it was easy to dismiss what was right there on the screen. Needless to say, much the speculation surrounding Jacob and Locke was somewhat off the mark.
This episode actually begins to explain some of the symbolism built into the series since the very first season. Going back to the earliest episodes, there was a constant reference to black and white stones, representing a light and dark side to motives, events, and the island itself. (Note that Jacob wears white; his rival wears black.) At the same time, Jack saw his father, seemingly brought back to life by the island.
After seeing so many apparently dead individuals return to life, most recently John Locke, it was easy to assume that Jacob was the one behind it. After all, Ben took Locke to Jacob's cabin, and it appeared that Jacob was using the form of Christian Shepherd. The idea that Jacob had taken on Locke's form, or had reanimated it in some way, seemed reasonable as an extension of those assumptions. And, of course, there seemed to be a relationship between Jacob and Cerberus, particularly the appearance of the dead to those about to be judged.
But now two and two have been put together, and the implications are a bit more clear (even if they are a bit more complex). The entity taking the form of the dead, and working in concert with Cerberus, is not Jacob, but rather, Jacob's rival. That rival has yet to be given a name, but he has been trying to find a way to kill Jacob and take control of the island for quite some time. This would appear to be the nature of the war that Widmore warning Locke about in "The Life and Death of Jeremy Bentham". At any rate, it certainly explains why "Locke" was a lot more focused and purposeful after his death.
The fact that Jacob and his rival both left the island in some form, leading those who would be on Oceanic 815 towards some greater destiny, strongly supports the notion that Oceanic 815's crash was not the simple accident that it seemed to be. The notion that Desmond accidentally made the plane crash was never satisfying, and now there are two layers that debunk that explanation. It's already been made clear that Widmore was responsible for ensuring that the plane was off course in the general vicinity of the island, and perhaps now the timing of Kelvin's escape attempt makes more sense.
The origins of Jacob and his rival are still unclear. The timing of the initial flashback seems to be roughly the 1800s, which would fit the theory that Jacob, Richard, and this new rival were survivors of the Black Rock. If so, perhaps Jacob's rival is Magnus Hanso, the first mate of the Black Rock. That would be a satisfying connection to the man behind the Dharma Initiative! (Alternatively, the ship seen in that flashback could have been the Black Rock itself.) Of course, that doesn't explain why Jacob would be hanging out in the chamber under the statue (which appears to be of Sobek, the Egyptian god of protection and fertility), using a loom to construct a tapestry with Egyptian and Greek motifs. The tapestry points back to the possibility that Jacob, Richard, and this adversary come from ancient times.