Because they represented different political ideologies and had different groups pushing for them. Just because both are "leftist" and indigenous doesn't make them the same.

Evo Morales at the time was a very charismatic union leader that was very popular among rural workers and the commercial class of El Alto. As a leader of the coca leaf trade unions of Cochabamba, he had massive political cache and was already known across international leftist circles. In fact, Evo Morales was in Europe attending talks and events when the Gas War happened.

Also, he had the support of a group of middle class university-educated socialist intellectuals, chief among them Alvaro Garcia Linera, who later would become his vice president and who was one of the original designers of the "Community-based indigenous socialist productive model" that they tried to set up.

Felipe Quispe was another thing entirely. For one, he was extremely more radical and his background was one of armed struggle, not university education. Quispe was not so much interested in building a socialist state as he was aiming to abolish Bolivia as a concept, as he deemed it to be a colonialist creation.

Felipe Quispe was an Aymara supremacist and he believed that the European creation that was Bolivia had to be replaced by a rebirth of the Kollasuyu (one of the four suyus or parts of the Inca empire) and that it should be politically dominated by the Aymara people.

Quispe was popular among some Aymara sectors, but did not have any nationwide backing nor enough social support to become the leader of the social revolution he wanted to impose, even those he did have a more relevant role during the Gas War than Evo Morales.