From the end of the note I posted on Facebook:
In the Flash Sideways, at the end:
*Where were Michael and Walt?
*Where were Rose and Bernard, who had both appeared in the Flash Sideways earlier?
*What about Ana Lucia, Eko, and all of the other lesser characters? Ilana? Naomi? Arzt? I mean, Shannon and Boone show up...
*Why was Penny there with Desmond? She wasn't truly part of all of this. Daniel's mom was there, but where was Widmore?
*What becomes of Jack's son? How'd he get there? Did he ever really exist? Does Jack have to leave him to move on, or does that not matter because he never really existed?
*Claire is reunited with Aaron, who left the island. Why are Jin and Sun not reunited with their daughter? (So, Sun is pregnant, but it's not quite the same. Sun has met their daughter. Is she ready to "move on" without her?)
*What about Nikki and Paolo?

(LOL)
*Ben was there. Juliet was there. Where was Richard? He got a gray hair last night, but is he still immortal?
*Ben wasn't ready to move on. Was he wanting to spend more time with Alex? Or did he just need more time in purgatory (if that was what that was) because of all his evil deeds? If so, then what of Sayid?
*The island was on the bottom of the ocean. Did that really happen?
*Was the Flash Sideways supposed to be just a construct of their collective subconscious? Is it purgatory? Why do they have to be "ready" to move on? What's the point of landing there, instead of going right from death to the ultimate location?
Island questions:
*Michael came back to Hurley as one of the whispers, trapped on the island. We never got an explanation to that. Why didn't he go on to the Flash Sideways?
*Why was Demond stuck on the island pushing buttons in a hatch?
*What about the numbers? Why those numbers that needed to be pushed, in sequence? Was it just coincidence that they were Hurley's winning lottery numbers and connected to Rousseau's distress signal?
*Why couldn't women conceive/carry to term babies on the island?
*How many sets of Others were there? How did they get there? What did they want?
*Why did they kidnap Walt?
*Who built the four-toed statue? The temple? All of the carved pieces (like the "plug") down in the cave with the light in the end? All sorts of Egyptian symbolism, but no explanation.
*Was there no meaning to all of the "special" people? Locke, Walt, Aaron? What about the Australian psychic's ravings that Claire had to raise Aaron? Just meaningless ravings? A red herring?
*What happened to Lapidus' plane after they took off? Did they get back to the real world and live out their days? Was it their wreckage on the beach at the end?
*What happened to Hurley and Ben back on the island? What was their fate? The island's? Hurley drank the water, so something had to happen that he died.
*How about the wheel in the lighthouse? What was THAT all about? How did THAT work?
*How did Jacob, who didn't believe there was anything other than the island, leave the island to touch all of the candidates as younger folks? How did he know to choose them? How did he know what they would become? How did he know they'd all be on that one plane that crashed years or decades later because Desmond didn't press the buttons? (Or did that not REALLY cause the crash?)
*What about Richard's visits to people, like young Locke? (When he presented him with the knife and compass?)
*Does the island "select" people? Do pregnant women have some significance? (Jacob's and MIB's mother? Rousseau? Claire? Sun?)
*What was MIB's name?
*What was all that stuff about a virus or sickness infecting people? Rousseau talked about it. The Others had all sorts of medical injections for it. The temple people detected it in Sayid. Claire went a little crazy herself, but apparently recovered?
*Why was Smokey going around killing people? From the very first episodes, where he was yanking people out of camp and the pilot out of the plane, etc.? What was the motivation?
*What was the series of flashes that appeared in Smokey sometimes?
*Why did ash and the big pylons keep Smokey out?
*Why were the Others kidnapping people out of the camp? What happened to Cindy and the kids from the plane? Did we find them in the temple after all of these years as an Easter Egg only to have them immediately killed by Smokey?
*What was the deal with Ethan and Goodwin and all of their crazy evilness?
*Why and how did Ben have extensive dossiers on all of the Losties? Everything he did when we first found him at Dharma camp led us to believe he was very powerful and had a global network, but did that not exist? If not, how did that all happen?
*How did Ben come to lead the Others?
*Why did Ben steal Alex from Rousseau?
*Who were the people in the temple, particularly the Sensai and his Hippie friend? How did Cindy and the kids flash back in time to be with them?
*After the second electromagnetic event, when Desmond was flashing back to England, what was that? Was that Flash Sideways? (Death?) Time travel?
*The Dharma Initiative (bunnies!) and Farraday seemed to be interested in time travel and the island. What was THAT all about? And the island jumping around in time. What was that about, too?
*Why is the island invisible to radar and how does turning a strange wheel underground move it and drop the turner in Tunisia?
*So, I think we were told that Dharma were the ones who brought things like the polar bear to the island, but how did the polar bear skeleton end up in the desert? Was the appearance of the polar bear in Walt's (Hurley's?) comic book just a coincidence?
*Why did Ben recruit Sayid as his henchman after they left the island? Who were the people still trying to kill the Oceanic 6 (like the guy on the golf course)? And why?
*Who was dropping supplies to Desmond?
*What did Widmore want with the island? Why was he so at odds with Ben about it that it led to murderous intentions?
*Was Hurley crazy? What about all of the dead people he saw, on and off the island?
*How did MIB become Smokey? Yet, Jack and Desmond and Hurley all went into the cavern and didn't become smoke monsters. Why MIB? Why didn't Jack become white smoke?
*Does Vincent ever die?
I'm sure the questions will keep flowing, but the well of answers has dried up, like the spring when Desmond took the plug out, leaving just a rumbling, angry volcanic cavern, waiting to explode.