Zexion was running to escape from Sora, who had managed to see past his illusion. Illusions are very powerful, and I think that the other pains they can inflict (emotional/psychological) endure longer than the pain(s) that physical attacks can, btw. So anyway, Zexion was already weak by the time he ran into Axel and the Replica. Plus it was sort of a sneak attack. I suppose that if Zexion had a weapon that was meant to attack head on rather than from the side--the point behind his weapon is strategy, manipulation, and secrecy--he might have won. But he was tired, and he was outnumbered. Axel wouldn't have let him go alive, especially not after Zexion realized his intention to annihilate him. Axel couldn't have Zexion reporting back to Xemnas with information like that...
Scythes are better for head-on attacks. Lexicons ae better for attacks in the dark.
(Chakram, kunai, and tessen are better than both just because they're cooler--J/K--, and memory beats all.)
Kioku shita ka.