What was the point of showing the island under water in LA X?
It made the viewers think that the Jughead/Incident flash had created an alternate world and gave them material for speculation all season. The payoff for it as part of a post-live waiting room -- nada, or they would have shown it sinking.
Personally I don't believe the Flash Sideways was written to be Purgatory. It makes no sense as one. Only the church scene makes sense. I think they went a different direction. They have said in interviews that they hadn't written the Finale until much of Season 6 had aired. (i.e. they gave an interview in April, I think, that they still had to write it. Perhaps they were waiting to see what kind of response the FS got.)
What was the deal with David (Jacks's son in the sideways)? Was he completely imaginary?
According to Christian, everything is real, even imaginary things. All the relationships that we saw in the FS would be real Purgatory experiences, but not ordinary real world history. Jack was never married to Juliet and never even knew her in his non-Purgatory life, so he couldn't have had a son with her.
Why was Penny in the church, but not Daniel or Eloise?
Happily Ever After plotline closure (and see last question).
Why didn't Jack (on the island) get overcome by the EM after he recorked the hole? Why didn't he turn into a Smoke Monster?
When you make up your own show, you get to make up the Rules. These are Darlton rules. There can only be one smoke monster? Jack didn't have a dark side? Oh wait, he did. Jack hadn't been popped over the edge by Jacob? It's 2000 years later and the magic place is out of smoke?
#1 -- Jack needed to die in the bamboo forest to close the show, and the island needed to be saved. The End.
Was Widmore lying about having the plane booby trapped with more explosives? Who was the source of the original bomb, Widmore or Flocke?
He didn't say more explosives. He said since he got on island. He hadn't been checking to see if anyone had tampered with his booby trap. It wasn't a bomb, it was C-4. Flocke made into a bomb, which shows how resourceful smoke monsters can be on the fly, grabbing watches off bodies before they even know they will find the explosive material.
Did we ever see Boone have his revelation?
Boone and his revelation were a sacrifice that ABC demanded.
Why did Kate change her clothes at the church?
Because she had just delivered an imaginary Purgatory-born infant and got yucky stuff on her dress, or because Kate doesn't do dresses by choice.
Why wasn't Richard at the church?
Because the fan base demanded see the regulars from Seasons 1 that they loved. This included Shannon and Boone. Richard was already in the Finale. The freighter people weren't included, even though they were in the Alt.
Anybody who was shown with a restored memory flash was there. Note that Miles, Widmore, Eloise, Charlotte, Nadia, Alex, Danielle, Helen never had those flashes, and Richard was never in the Alt at all. Unfortunately for Richard, he never had a love interest with whom to flash, or he may have been invited.
Alternative explanation: When Jack replugged the island, Richard became ageless again and he never died, and in fact he still walks among us, working for Hurley and Ben, and when they pass on and go to the "has no Now" waiting room, he'll work for the next schmuck who takes the job, because it's what he knows and he gets to travel a lot.