I guess those were seen as a resource at first, back when they had little idea what they were doing (JJ Abrams: "I think what would be cool is if there was a hatch there")--more places from which to introduce new mysteries, more distractions for when they couldn't think of any, more human interest stories to keep ABC and the ABC-type viewers happy. But yeah, a point comes when a lot of them get in the way.

They tend to recognize this and 'spend' uncentral characters with sacrifice-type plotlines--Shannon and Boone, Charlie, Ana-Lucia, Eko, Michael. They do need love conflict stuff happening, that and revenge are surefire, easily-written short term interest creators (like unrequited passion's the moneymaking long-term one), so Sun and Jin are going to stick around. They put Claire and Walt on the backburner because the child stuff is near the heart of the plot--they'll figure heavily in the last half of the last season, presumably.

Keeping both commercial and cult audiences interested at once can't be easy.