I liked it.
The only standard is that the rules of the universe within Lost (once accepted) are played by. I don't think they broke those rules.
The island itself is two things:
1. The spiritual element - the light, the temple pool, etc.
2. The scientific element - the E/M
Both sides are valid - the root of the light may indeed by spiritual, but the manifestations are indeed physical. It's why Daniel Farrady could understand so much about the island, even though he couldn't comprehend it's spiritual side. And it's why even those who embraced the spiritual side (let's say Locke) - couldn't really understand the island. Not even Jacob fully understood the island - he didn't know how to kill MIB, and he didn't know certain things his "mother" did, like how to make it so MIB and Jacob couldn't kill each other, etc. Being the "Jacob" was also no recipe for being a better person. He still "killed" MIB by throwing him into the light - "would I die? no - something worse than Death." Remember that his mother thanks MIB when she is killed, and also apologizes before killing their real mom. At the same time - she is flawed... killed the real mom, kills the villagers, thinks everyone is bad, won't let MIB leave. I think MIB could have left up until he became smoke monster.
Dharma was a bunch of scientists - they were trying to exploit the island resources - but they didn't know that much about the island.
The others are just people that had been brought to the island (either by Ben), from Dharma (like Ethan), by chance (like Alex), and probably by Jacob. The island seemed to slow aging so it makes sense that the group would grow overtime - and a band of others already existed when Dharma was there. Pregnancies turned out fine until some time between the nuke set off by Juliet and sometime well before they get Juliet. I'd go with the nerve gas murder as leaving some toxins behind that cause the problem, but the nuke could have done it too.
Generally the mystery of the island is greater than the show - we don't know who did all the carvings, built the temple, put the stone in the fountain in the cave, built the tunnels and special stuff under the others, etc.
In terms of the ending - I don't think you need to over think it. By the end of the show, those main set of characters had been redeemed, but were not necessarily ready to move on. They still had some issues that had to be resolved and the sideways flash presented a real challenge, it made them superficially happy. Jack is a father, on good terms with his own father's flaws, working hard and liking work, on good terms with his ex. You could say superficially these are the things he'd want, or reflect what he believes about himself to make himself happy. (Almost like the Tom Cruise and Penelope Cruz movie where he has a comfortable existence in virtual reality and can wake up if he does something he chose as the exit.)
The sideways flash is like the opposite of Micheal's existence, where he's trapped as a ghost in the real world. The "redeemed" are trapped as real people in a fake world. But just like the Ghosts can sometimes make contact with the real world - through Hugo for instance, Desmond is still able to flash to the sideways world. Desmond essentially accelerates their exit by bringing the people together, eventually Hugo might have met Libby. Etc.
The other thing the writers did is by making the sideways flash purgatory (of sorts) they put to rest the claim that the island is purgatory.
Was it perfect? No. There were probably about 25-30% too many episodes, but the writers didn't know which way to go at times, as much as the audience is moving with the story, so are the writers. Could we have done without the temple subplot? Probably. Etc.
One other observation - Sayid leaves Locke and redeems himself, even though the temple guys said he was evil and become more evil. What's the answer here? Free will triumphs "destiny".
