Wing Commander Academy is *not* about the Terran Confederation Space Naval Academy -- none of it (not even the first episode!) takes place there.
The first episode, "Red and Blue" takes place at the Flight School on Sirius, *after* Maniac and Blair have graduated from the TCSNA on Hilthros. They've already gone through the Naval Academy, Blair has done his training on the Formidable, they've graduated. At the end of Episode 1, they learn that they're being assigned to the TCS Tiger's Claw.
This is where the movie opens -- Blair and Maniac being transferred to the Tiger's Claw (they'd been delayed according to the movie novel, which is why the other cadets aren't with them on the Diligent). The movie takes place, Pilgrim Stars takes place, Pilgrim Truth takes place, WC1 starts.
The *rest* of Wing Commander Academy centers around the 2654 Sivar ceremony, which takes place *later* in WC1. The term 'Wing Commander Academy' refers to an advanced command school, and *not* the TCSNA. This is actually explained in the press kit. The other 12 episodes take place, at the end of which Blair is made a squadron commander... and then WC1 can ends with him commanding the Black Lions.