I want to start by saying I'm a HUGE fan of Lost, have been since day 1. And I'm only analyzing these plot points to see if anyone shares my frustration on these few particular topics...
There are three huge plot holes in Lost that have been driving me nuts lately. The first and most obvious (which has been discussed numerous times already), is the whole Charlie/Desmond flashes storyline. Charlie gave his life to save Claire, based on info he received from Desmond. Yet Claire was never taken off the island in a helicopter, and Charlie has seemingly died for nothing. At the time, it was one of the most fulfilling & emotional storylines in Lost history... yet looking back on it, seems rather disappointing. Why didn't the vision occur as all the previous ones had? Was Desmond simply lying to Charlie to get to Penny? Was his vision wrong? Why doesn't he seem to care? Either this will be answered in the final season, or Lost will have failed to follow up on an enormously important plot point.
The 2nd is Ben's backstory. In season 3, Man Behind the Curtain explored Ben's childhood. When he bumped into Richard in the jungle, he was told to be "very, very patient" if he wanted to join the Others. We later see Ben all grown up, still living with Dharma, and eventually leading the purge and killing off the entire Initiative. This scene, and episode as a whole, was extremely powerful. It lead us to believe that Ben waited years and years, living with his father in Dharmaville, until the time was right. However, in season 5, Ben was shown sneaking out and living with the Others at night time, hanging out with Widmore, and really hadn't waited very long at all. The whole 'patience' attribute of the character was completely lost, and makes the classic Season 3 episode so much less fulfilling. Why mess with something great? Why add unnecessary pieces to an already-established backstory if it negates an earlier tale? Now we know that being 'very patient' was really just a couple of weeks until he was apparently accepted into the Others' community. Man Behind the Curtain has been cheapened beyond repair.
The 3rd, and least bothersome, is the conversation between Jack and Locke off the island. Jack clearly stated that he had been all miserable and yearning to go back due to his conversation with Locke. According to Jack, the content was along the lines of, "he told me that some very bad things happened after I left, and it was my fault for leaving, and that I had to go back." However, when we flashback to the scene in Season 5, we see Locke tell Jack absolutely nothing about bad things happening because he left. We heard "your father says hello" which seemed to really rattle Jack, and seems to be his motivation for going back. So what is Jack's true reasoning? Why does he want to come back? And what happened between the season 4 and 5 finales that made the writers and producers completely change their mind and write off the inconsistency without any form of explanation?
I've rambled too long. Anybody with any opinion on any of these topics, please share your thoughts. I'm very curious what the rest of the Lost community thinks about these subjects. Namaste.