Season 2 ended in a reboot.
Season 2 introduces the tailies. They are all subsequently killed (except for Bernard).
Season 2 gets us into the hatch. The hatch is subsequently blown up.
Season 2 introduces the necessity of entering the numbers. Not entering them has no legitimate consequences.
Michael spends the entire season looking for Walt. Once found, we are never told why Walt was important to the Others.
Season 2 shows us a map of the island in the hatch. We are never told how this map happened (nor why a smoke monster needs "vents", given what we now know about the smoke monster).
Season 2 ends with Penelope finding the island. But then the boat that shows up is "Not Penny's".