Never filmed Star Trek: Voyager scene had Captain Janeway considering a field commission for Neelix
Neelix was a very controversial character for Star Trek: Voyager. While many fans enjoyed the quirky energy of the ship's only Talaxian, others found him to be intrusive, too exuberant, and downright annoying. I think that was part of his charm. The actor, Ethan Phillips, played the part of an unofficial assistant to Captain Kathryn Janeway (Kate Mulgrew), and he didn't only irritate the audience; he irritated the crew. But, according to a scene that was included in the shooting script for "Eye of the Needle," which aired during the series' first season, Neelix was having a conversation with Kes (Jennifer Lien) during which he told her that the captain had considered giving him a field commission which would have put him in a Starfleet uniform.
According to Giant Freakin' Robot, this was just part of the talk. The other focused on Janeway's supposed comparison of Neelix to Sacajawea, the Native American who helped Lewis and Clark on their journey through the Louisiana Territory. Though Neelix was supposed to be helping Voyager make its way through the Delta Quadrant, his assistance actually didn't occur that often. He certainly didn't help anywhere near as much as Sacajawea did for Lewis and Clark. Not only was this reference omitted when the episode was filmed but so was any indication that Captain Janeway would be offering Neelix a field commission.
Can you imagine Neelix as an officer in Starfleet? He wasn't the play by the rules type of alien, and that made him a better character. The entire ship couldn't be about rules and regulations. Neelix offered something Starfleet officers couldn't—a way of looking at each situation through an unfiltered gaze. Though he submitted to Captain Janeway's authority, he didn't follow suit with the other onboard officers like Tuvok or Lt. Paris, which often added some extra dissension.
Neelix might have been disliked as a character, but, in a way, that was a good thing. The series needed another character that viewers could either root for or dislike as the crew of Voyager was overall accepted and well-liked. Adding Neelix to the Starfleet roll would have taken the character in a different direction, one in which he didn't fit.