I've been typing up my thoughts since last night, and based on posts made thus far, it seems I share a lot of the same ideas as everyone else. Always good know I'm not totally in left field.
And if it comes down to a vote, I vote for Dr. Evil as the Lost and Gone for a While official name for Man #2.

Thoughts:
• Jacob and Dr. Evil – was that a great opener or what? Do we think the ship they were observing off shore was the Black Rock? If so, does that put us any closer to placing Richard “Ricardos” Alpert on board as either its captain or a member of its crew?
• Season 5 is (allegedly) supposed to mirror Season 2. If that’s the case, Ben in Season 5 is Locke in Season 2. What I mean is, at the end of Season 2, Locke made a choice and destroyed the computer in the Swan Hatch. He thought he was doing the right thing, but in fact he almost caused the second incident. It forced Desmond to activate the failsafe and blow the Swan Hatch to smithereens. In Season 5, Ben was brought to Jacob and had to make a choice: kill him or walk away. He chose to kill Jacob thinking it was the right thing to do. In essence, he broke the computer. The question now is what are the repercussions of Ben’s actions? Will the giant foot blow up transferring power to Ben so that he can see when Richard is going to die a la Desmond and Charlie? Probably not. My guess is Ben has now disrupted the equilibrium between Jacob and Dr. Evil by tipping it in Dr. Evil’s favor. Perhaps this unleashed the war that Charles has been talking about. But a war for what? The Island? Humanity’s survival? Jacob’s beachside condo?
• I agree with what some people have been saying about Dr. Evil being Christian Sheppard. Since dead is dead, Christian died in Australia and Dr. Evil simply took on his appearance after the crash of 815. I’ll take it one step further and state the obvious: Dr. Evil can somehow impersonate other people. Hmmm. Who else can do this? That’s right: Smokey!!! I think Dr. Evil is the smoke monster. I imagine there are some inconsistencies, but it seems to make sense in light of recent and not-so-recent events:
o When Ben visited Smokey in the cave beneath the temple, Evil Locke conveniently disappeared in search of rope so that Ben could have some quite time with Smokey and Alex. I look back on this moment now as though it were lifted from a Superman comic. Clark Kent conveniently disappears at the very moment Superman is needed, but everyone knows Clark and Superman are the same person. At the cavern under the temple, Clark and Superman are represented by Evil Locke and the smoke monster…only they’re bad guys. As Locke, Dr. Evil was able to get Ben into the cave. As Smokey/Alex, he was able to convince Ben to do whatever Locke wanted him to do. All Dr. Evil had to do then was become Evil Locke again and march Ben off to the statue.
o In previous seasons, Ben is perceived as being able to call upon Smokey for help. At least, that’s how it appeared. It makes more sense that Smokey was simply making himself available to Ben while he was in fact manipulating Ben the whole time. He was building Ben up, making him feel empowered and in touch with the island. Kind of changes the way I look at Alex’s death in Season 4 and the way Smokey attacked the mercenaries.
o Locke had his face-to-face with Smokey in Season 1, an event that seemed to set Locke on the path to finding his destiny on the island. Perhaps that was simply Dr. Evil (in the form of Smokey) setting Locke along the path to being part of his loophole plan.
o How might this change the way we understand Mr. Echo’s death? Did Smokey/Dr. Evil kill Mr. Echo because of Mr. Echo’s influence on John Locke? Was Mr. Echo dangerously close to detouring John from his path along the loophole plan? I’ll have to rewatch the events of Season 2 and 3 concerning Mr. Echo, but I bet his life on the island will take on a new level of significance after last night’s finale.
o Concerning other people Smokey has killed: what about Danielle’s friends? What about the pilot of Flight 815 who wasn’t supposed to be flying the plane?
• The Cabin – so the cabin was in fact some sort of holding cell and the ash around it was acting as a kind of restraint or seal. I’m not sure I fully understand who was in the cabin before Season 5. I want to think it was Dr. Evil, but Ilana’s actions make me think that at least she thought Jacob was living there. Here’s why: Ilana and Bram brought John Locke’s body to the cabin before taking it anywhere else. They brought it there as Bram explained to Frank because they had to show it to someone. When Frank asked why, Bram responded, “So we can show him what he’s up against.” It would make more sense in my mind that they would want to show John’s corpse to Jacob so that Jacob knows his latest leader has been killed by Dr. Evil (if John was in fact supposed to be the latest leader). Therefore, it seems they thought Jacob was in the cabin all along. When Ilana says to Bram that the person they’re looking for isn’t inside, she follows up with that nugget comment of “Someone else has been using it.” I can only assume that Dr. Evil was that person. Clearly, I’m not completely confident with my understanding of the cabin yet, so I’ll wait for Brian’s analysis and everyone else’s comments before settling on this issue.
• Bernard & Rose – I don’t know about the rest of you, but I love the way the writers addressed Bernard and Rose. “We’re retired.” Love it! This gets me thinking that if for some strange reason Bernard and Rose, with their inner hippyness in full effect, are now exempt from any more time traveling and won’t jump with the other survivors at the beginning of Season 6, that they’re now set up to be Adam and Eve (the skeletons at the cave from Season 1).
• Kate, Juliet & Sun – overall, I was very disappointed with the way these characters were treated in the finale. And with Sun in particular, her development this season was virtually non existent. But the whole back and forth mind changing by Kate and Juliet over whether to help Jack was just ridiculous.