One of the great unsolved mysteries of LOST is the Island.
Some believe that the Island was its own character. That it may have been a supernatural being in its own right - - - so foreign to modern humans as to be "magic."
Others have tried to rationally explain the Island.
We know of few facts about the island:
1. It can move. During Faraday's rocket test, it was shown that the island was moving away from the ship. A real island cannot move across the ocean.
2. It had special light properties. When Faraday landed on the island, he remarked that the light was strange, that it may be bent. One of the theories of stealth technology is that the bending of light and reflection could cause an object to "disappear" to the naked eye. When the helicopter left the doomed freighter, Jack and those on the copter saw the island vanish without an ocean ripple.
3. It has unique electromagnetic properties. The Swan station was created to try to manage the EM properties so the island would remain in balance. When it was not in balance, the large purple flash would occur sending the island out of phase with time or space.
If you tie all three of these facts together you can come up with a plausible theory.
The island was a UFO.
Since earth islands are volcanic mountains that begin at the base of the ocean to crest above the water line, they do not move. Therefore, the Island is not an island.
Electromagnetic energy can be used as propulsion system. Several countries have been using technology to support monorail trains riding on a cushion of magnetism. The movement of the Island could be made as a result of the electromagnetism. This means that the Island has a powerful engine, probably underground in the forbidden zone, which allows the guardian to pilot the island to safety.
Stealth technology is also researching the use of bending light waves to mask radar patterns. Magicians use mirrors to make things disappear by light wave cancellation techniques. In a larger scale, the Island could mask itself by using EM energy to "bend" light waves to make the island disappear.
So what would be the purpose of a space alien having a stealth UFO in the Pacific Ocean?
Just as in other sci-fi shows like Star Trek, advanced space travelers would often create "observational posts" on primitive planets to gather data on the inhabitants, cultures and technology. A UFO disguised as an uncharted island would provide cover for any human wandering to it.
Further, mere observation could lead to more advanced testing and experimentation on humans. It was said that the guardian was the only person who could bring people to the island. The guardian must have been the captain of the ship. What better way to observe how humans interact than putting them in a survival situation on a dangerous island?
What would space aliens gain from such encounters? Information on human behavior, science experiments including DNA enhancement, mind control tests and possible allies in the off-island world. Wealthy people like Widmore may have been recruited by the Island aliens to obtain information that they could use (especially in defense technologies). The aliens could have given Widmore technology to make him rich, and in turn Widmore used his wealth and power to provide the Island with any resources it needed to survive, mostly human subjects.
UFO researchers believe that since the atomic age, at least 60 different space aliens have visited Earth and have been in contact with national governments. It may be too difficult for isolated ships to "conquer" the planet. But it probably easier to infiltrate world governments if aliens are after the planet's resources, such as gold which many scientists believe is a key element in deep space travel.
The UFO theory in LOST also answers the question about the long life of Jacob - - - he was not a human being. The smoke monster was not a human being. The aliens tried to breed human-alien hybrids on the island but those experiments failed (and why Juliet was summoned to the island). Space aliens could colonize Earth by interspecies procreation which would take human elements (compatible with Earth's environment) with the longevity of the alien races.
The UFO theory also can support the reason why Jacob and MIB wanted to "leave" the Island - - - they were so far away from their home planet their mission was a death sentence. They would rather die and end their existence than deal with the "never changing," corrupt and primitive humans.
Finally, with the real aliens gone, the Island ship would have been scuttled - - - which would explain the images of the Island resting on the ocean floor.
The Island as a UFO has some merit as being a plausible premise to the series.