[Teuthida]

Pretty much everything mentioned in that video above (although some of those can actually be answered if you think about them).

The numbers. They made them out to be so important and holding such great power. They explain it away by saying Jacob had a thing for numbers. That doesn't answer squat.

Walt. Had powers (Hurley and Miles also had powers but everyone passed talking to the dead off as normal so it's not really a mystery) which scared Ben and Juliet so much (not sure if that scene was in the main show or just online) that they let him go after trying so hard to acquire him.

Ties into the list of the good and the bad (which is why I also think they originally had the island set up to be purgatory but changed it...the children not being able to be born there would fit nicely with that too).

Locke being able to walk. Rose's cancer disappearing. Just the healing properties of the island?

Baby Aaron. There was so much damn focus on him. Nothing ever comes of that. He was born (after many attempts by the others to kidnap him and Claire), taken off island, and is seemingly a normal kid. He also figures into the whole kids not being able to be born on the island. One could say it was the nuke that prevented this (yet Richard knows about the nuke and still gets Juliet to come to the island to figure it out). It probably goes back further since that four toed statue is a fertility goddess.

Mostly I'm angry that they never had answers to how things worked: The donkey wheel which both moves the island and teleports the person pushing it...and is somehow frozen (which makes sense why they used polar bears...sort of...but still never to explain why it's frozen), MIB turning into the black smoke (yet Jack could chillax in the magic jacuzzi and come out normal...is it because he's now like Jacob?), explaining away everything by saying someone is "special", immortality and all of Jacob's powers and ability to share them.

Basically the whole nonsense with the light and evil escaping (MIB never came off as being evil incarnate). Why did Jacob have Richard and the others kill all of the Dharma initiative if he's the good guy?

Argh, basically nothing makes sense. No wonder they choose to ignore everything. Everything was poorly thought out.


EDIT: Hell for the whole donkey wheel thing all they had to do was show someone or something near the light, have the area freeze over slightly and disappear...and maybe reappear somewhere else on the island. MIB could deduct having an external wheel could maximize that power and leave the island. But no. We get "I'm special."

EDIT 2: And I get not explaining everything to leave things up to the viewer...I'm fine with that...but instead they make everything so final trying to explain away everything with a magic light and being special...and then have everyone die that one can't assume those mysteries are ever discovered.

EDIT 3 (to your edit and previous mention): Abrams didn't have anything to do with the show past the first season.