Yeah, naming the kid after Charlie makes the most sense since Desmond and Charlie had a unique thing - in a funny sort of way, Desmond was able to "save" Charlie after all.
As for last night's episode, there were so many things happening again that it was just crazy - where did the strange boats come from? Who was shooting at them? How the heck is Jin (knew he wasn't dead) going to explain himself to Russo and the Frenchies (makes me want to go back to some of those episodes and see if Russo ever reacted/interacted with Jin in those eps)?
I'm loving this season so far - the off island stuff, the on-island stuff, time travel, time paradox, etc - this show is frickin' sweet.