Becuase the game already had a Gunblade user and SE was afraid Seifer would play too much like Squall, that's the actual reason they gave but he was actually their first choice until someone on the team mentioned the problem. Technically, if you pay attention to Squall's animation for his attacks he actually uses it one handed like Seifer.

The list of character who didn't make it but were actually considered are: Kain Highwind, Locke Cole, Seifer Almasy, Yuna, Seymour Guado, Prishe, Vaan, Balthier, and Lightning.

Here are the reasons stated:

Kain Highwind - Not really a villain and they felt Golbez would work better from a story standpoint. As a nod to him, Cecil has moves designed to emulate Kain

Locke Cole - Terra is actually Nomura's favorite character and they wanted a female on the Heroes side. The main reason was because Terra had a stronger connection to Kefka than Locke.

Seifer Almasy - Too similar to Squall, like Kain/Cecil, Squall has moves where he fight one handed like Seifer.

Yuna - Because Seymour wasn't chosen as the villain and they felt Tidus was more of the lead hero.

Seymour Guado - Cause he doesn't have any real relationship with Tidus, Yuna then began to be considered as the new hero but they stuck to their guns and kept Tidus the lead.

Prishe - was the original character chosen to represent XI but was scrapped for Shantotto, though no official reason has been given why Shantotto was chosen instead, most fans theorize its because the Tarutaru are the more recognizable race in the XI universe.

Vaan - No reason is given except that he was apparently rejected by the staff in favor of the other candidates. Funny enough, Penelo makes a mention of this in the Battle Tip section.

Balthier - Passed over because he had already appeared as a guest character in Final Fantasy Tactics: The War of the Lions.

Lightning - The team decided that they didn't want to release info on a character before her game hit shelves.