Yeah, Desmond is the only exception to the rule, but even his influence is fairly short-sighted. At best he can delay fated events. He can't prevent them altogether though. For example- Charlie. Desmond saved Charlie an assload of times but ultimately Charlie was killed. At the same time, Desmond's intervention must have also been fated as Charlie's death by drowning has been foreshadowed since season 1.
So far the only contradiction/mysteries that remain regarding time travel on lost are these 2 events:
1) Claire and Aaron not leaving on a helicopter as Desmond promised.
2) The way the 06 are split across time on their return to the island via Ajira 316.
One of the question's I've put up on Lostpedia (good wikis, retarded forum) to be presented to Carlton Cuse/Damon Lindelof for an upcoming interview they'll give is regarding the nature of Desmond's uniqueness and whether it was due to his destiny or his time spent in the hatch (that resulted in high exposure to EM energy, etc).
There is a convincing theory I read recently that contended that Desmond had gotten his special time manipulation abilities from staying in the hatch and that Daniel's future in Dharma revolves around him going to the Swan and trying to replicate Desmond's experience so he can change time and save Charlotte. But his desperation will make him screw up and initiate 'the incident'.