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No Plans, No Prototype, No Backup: Played With. The Excalibur was actually one of two prototypes, but the Victory was destroyed saving Earth from the Shadow Planet-Killer. The Drakh also destroy the shipyard where both vessels were designed and built, so while the Alliance will be able to build more eventually, it'll take a few more years.
Obstructive Bureaucrat: Inverted: The project lead (Drake) is dragging his heels with the excuse of trying to get all of the ships' systems running perfectly, while Garibaldi, the administrative head of the project, is pestering him to just get everything "good enough" and let the ships' crews iron out the wrinkles later.
Not really poorly disguised, as it was deliberately made and promoted as a lead-in to Crusade.
Posthumous Character: The Drazi captain, who dies before he can actually join the party. He leaves behind some valuable intel for the others to find.
Pyrrhic Victory: The Planet Killer is destroyed but the Drakh manage to release a plague into Earth's atmosphere which will kill the entire population within five years.
Retcon: Previously the Shadow Planet Killer had been depicted as a cloud of missiles. In this film it is established as having a solid superstructure concealed in the cloud.
Revenge by Proxy: Sheridan convinced the Shadows to leave the galaxy, and by extension could be seen as responsible for the destruction of Z'ha'dum, the Drakh's adopted homeworld. The Drakh, not happy with their demotion in the grand scheme of the galaxy, decide to destroy Earth in revenge.
Self-Deprecation: A bit of Meta Humor: Garibaldi tells Sheridan that if he wanted to watch a screen full of nonsense, Garibaldi could show him some 20th century television.
Slipped the Ropes: Never taunt an escape artist about being restrained, especially if she has training in unarmed combat.
Transhuman Treachery: Drake against Earth, because of the discrimination against Mars-born humans. Ironically, he was only in a position to act on this because Earth-borne Garibaldi hired him based on his merits rather than social connections.