I think that the main problem with the show was not the finale as such, but they probably made the mistake of dividing the mythology stuff and the scientific stuff into different seasons. I think that most of the answers as to what the island is lie in season 5 actually. It may be some sort of egyptian-gaia-origin of life-evil vs good- stuff, but I think most of it is about sci-fi.
I am no scientist but I think the last few episodes have shown that the multiple universe theory is probably the closest to the true answer. The electromagnetic light and the island itself acts as some sort of force that keeps the universes from colliding to the point of their own destruction. When you remove the "cork" the light is released and the force keeping them intact is released with devastating consequences. Maybe in mathematical terms the island is a string of variables that keep all universes in harmony, with the constant being obviously desmond.