My favorite is Wing Commander IV
But i never played Privateer 1, Academy and Armada, so i can't say how good/worse they are.
And Privateer 2 hasn't a connection to the WC Universe. I'm not sure that this game plays in the WC Universe, at all.
But i like all Main-Plot Wing Commanders, so WC1 to Prophecy - Secret Ops.
Wing Commander I was my second game after Frontier - Elite 2 i play at an Amiga 500. So i have a special connection to this series, because it was my second game, at all
The only thing i dislike is, that they cut the cockpits out of the game after Wing Commander 3. Only a FS-like HUD in WC4 and Priv2 and a FL-like Cockpit in WCP and WCSO
But for the Story, WC4 was the best. It was a good movie. Okay, maybe it need a few more missions. But it was a good game. And i like that this game a multiple endings and you can decide if you join the border worlds now or later