Regarding the alternate timeline: There are some distinct bizzaro world differences like Desmond being on the plane and Hugo thinking he is the luckiest person alive. Not to mention... Jack seems like he remembers everyone.
yeah...i was definitely getting a vibe that jack remembered...also, did boone's comments mean shannon wasn't on the plane?
Jack had actually met Desmond before when they were running at the stadium, and I was surprised they didn't acknowledge that.
I'd wondered the same thing about Boone's* comments, although it just now occurred to me that things wouldn't necessarily (nor should they) be exactly the same if they had succeeded in changing history. Some of the Pre-Season 1 events might've depended upon The Island in some unforeseen way. However, if you think about it, some of the changes should be expected. Hugo's numbers, for example, might not be cursed without their association to the hatch, or for all we know, he would've played different numbers since the man he was supposed to have heard them from in the asylum wouldn't have been obsessed with them. In fact, it seemed that Hugo had gone to Australia for a completely different reason this time.
Along that line of reasoning, I suppose it's entirely possible that Jack and Desmond hadn't met in the stadium in this timeline. Widmore might not have left The Island (would he still have been exiled by Ben?) or survived the explosion, so even if Penny were still conceived, there wouldn't have been a boat race for Desmond to enter and train for. Maybe Jack started to remember Desmond simply because "the rules" for paradox still don't apply to him.
Did John Locke embellish the walkabout to Boone to save face or did they really let him come along this time?
*Speaking of Boone, I LOL'd when Jack actually wanted a pen for an emergency tracheotomy, as he'd let Boone believe in Ep. 1.1 just to get him out of the way.