The show's "native" people were not actually island natives. It seems that everyone on the island was brought to it by Jacob or his de facto followers. In Ben's reign, the Others were merely rebel Dharma-folk cloaked in the Others tribal costume.
A better alternative would have been to have the Others really be island natives who would naturally fight any intruder to their space.
A true small Pacific island would have limited natural resources. If suddenly 48 survivors begin to live on the island competing for food, water and shelter, the two groups would clash over resources. It is only human nature. Even a self-sufficient non-technological tribe has the will to survive against modern, technologically advanced people.
The alternative Others story would eliminate the need for scientific side arcs like the chemical weapons purge, the island's mysterious EM life force, the Hatch, the Numbers and the political diversions of the tussle between Ben and Widmore over the control of the island, and the Jacob-MIB story arc. It would be pared back to a bare knuckle survival story.
The alternative Other's leader, a king and cult figure to his people, could be as ruthless and cruel as Ben and Widmore combined. That could be represented by him wearing a child's skull as a necklace (even though it would be hard to get that past ABC's prime time censors). You could add horror elements such as cannibalism, devil worship, tropical fever-madness and revenge warfare as concurrent themes of the natives as they push back against the invasion of Westerners.
Jack's group would be cast as a serious underdog in such a fight. Jack and the beach camp don't know the island and its resources. They are backed up against the beach without normal defenses (except one gun and six bullets). Can one man's military training and one man's delusional outback hero fantasy be enough to keep a violent native tribe at bay?
It would have been a pretty good story.
You could even capture a few of the early dropped elements of the Other's story. If there was an infection, could Jack save the natives and thereby saving his own group from genocide? If there was an issue of tribal women dying in child birth, could Jack save the babies and thereby saving the island population from fading away? Or if the island women were barren by the infection, would the Others kidnap the women and children in order to keep their genetic lines in tact (again, human nature is to reproduce another generation in order to survive)? These real tribal problems could give rise to the plots that the survivors are the solution to the island's issues - - - from medical knowledge to breeding stock.
There would always be some faction in the beach camp that would want to attack and counterattack the Others in order to forge a place on the island. Another faction would want to seek a peaceful alternative. It is this flashpoint of opinion that could lead to drama, in-fighting and betrayal within the survivors' camp. There also could be a certain madness that would seep into those characters since they have been entitled, pampered, technology dependent individuals who have had their worlds turned inside out. Faced with a real threat by the natives, there would have been an urgency to get off the island and get rescued.
As for the filler arcs, a strong native population could have a back story of actually taking down earlier island visitors such as the U.S. Army (and worship the Jughead bomb as a iconic god) to a bizarre twist that one of the mother elders of the tribe who speaks English is none other than Amelia Earhart.
As a group, the Others were underwhelming in the original series. It was organized more like a street thug crew than as a cohesive group. It could have been used as a more dangerous adversary than as Ben's criminal followers.
