He has Crohn’s disease, ulcerative colitis or another digestive disorder.
This would explain why he would have spent the entire flight in the bathroom and why his bathroom trips in the jungle were so lengthy, yet he did not want to discuss it.
He was doing something inappropriate in the jungle not suitable for network television.
He was part of a different faction, not an Other and not a follower of Jacob but perhaps a follower of the Man in Black.
During his "trips" he was following a vision of some kind.
Nathan was a drug addict who had his stash on him during the crash, and he was getting his fix during his trips away from the others.
Nathan was simply a jerk with an antisocial personality who had trouble with authority figures and thus resented Ana Lucia taking charge.
Nathan exhibits traits of a person with antisocial personality disorder, including hostility, arrogance, dishonest behavior and a lack of empathy. He never appears concerned about the other survivors or those who have been abducted. Unnecessary risk-taking is also one of the symptoms: his two-hour bathroom breaks could really have been him exploring the island by himself.
This type of personality disorder would likely have led to run-ins with the law in the past, which would have made him most unsuitable ("not a good person") in Ben's eyes. Nathan would have immediately challenged Ben's leadership and mocked the Others' blind devotion to him and faith in Jacob.
This antisocial personality theory is supported by the scene in which Goodwin "rescues" Nathan from the pit: Goodwin tells Nathan he is rescuing him because they are afraid Ana Lucia is going to hurt him, and then gives him food and tells him which direction the beach is. Nathan never says thank you or exhibits any sign of gratitude.
Nathan had a criminal past and was doing something illicit in Australia, such as smuggling drugs or weapons. People with criminal records and criminal associations are not allowed to enter Australia (a major plot hole in Sawyer's story), thus, he would have had to be traveling under falsified documents.
It's well known that every other reference to Canada or being Canadian in Lost, is indicative of deception. It stands to reason that Nathan may not actually be Canadian at all, or if he is (which would mean he is the only true Canadian in the entire series), then he was being deceptive in some other way.
It's possible, but unlikely, that Nathan was indeed an 'Other'. This does not mean he wasn't on the plane (there is little evidence either way) - adding credibility to him potentially being Widmore's victim, or the person who was holding the camera. His long disappearance may be the result of him meeting one of the Others secretly to give them the video tape (that was later shown to Locke by Ben).
This does not explain however why he was referred to as a bad person by both Goodwin and Ben. One theory is that (while previously living amongst the Others), he took a liking to Juliet. As Goodwin was having an affair with her at the time, and Ben's affections for Juliet well known, their individual jealousy could have led them to believe he was 'bad'. Another reasonable theory is that Nathan somehow conspired with Widmore in some way. If he was Widmore's victim, he may have divulged information to him that he was not supposed to (perhaps under duress/torture).
If Nathan actually was an Other, Goodwin and Nathan would have known each other. In the scene in which Goodwin "rescues" Nathan from the pit in the middle of the night, Nathan at first appears suspicious when Goodwin throws down the rope. The conversation shows Goodwin continuing to play the part of one of the tailies. Additionally, Nathan has to ask him in which direction the beach is. If he were an Other, Nathan would have known the Island inside and out, and would not have needed to ask this.
Ben's instructions to Ethan and Goodwin are for them to immediately blend in among the survivors of the plane crash in order to gain their trust, in order to accomplish their goal of taking any "good" people, children and pregnant women. It would not serve much of a purpose to send an additional person who would do the opposite by alienating the survivors and making them paranoid that someone among them was a spy.
Nathan is not seen at all during the crash/rescue scenes. We first see him exactly 10 minutes into the episode 'The Other 48 Days', right next to Ana Lucia and seconds before several Others are heard nearby waking up the survivors as Eko kills two of them (triggering his 40 days of silence). This is not to say that Nathan appeared to the survivors for the first time at that point - but the fact WE see all the others in the initial crash scenes except Nathan seems a deliberate tactic on the part of the writers.
Watch carefully at the looks that Goodwin and Nathan give each other thoughout the episode. Some of the looks could be interpreted as some sort of familiarity with each other - which over time turns into looks of frustration. Was Nathan purposely deflecting attention from Goodwin so he would not be caught out by an increasingly paranoid Ana Lucia?
He does not seem to sound Canadian. When first put in the hole by Ana Lucia, he yells 'let me out' several times. There's absolutely no evidence of accent at all! (Canadians have a very distinctive way of pronouncing the word 'out').