The thing that got me about Academy was that Blair and Maniac served under Tolwyn, not Halcyon. This made me confuse Halcyon and Tolwyn for the longest time.
If memory serves me, we never actually meet the captain of the Claw in the game. We only see Halcyon who is more of a Carrier Air Wing commander rather than a ship's captain.
The captain of the Tiger's Claw appears in Freedom Flight and his name is Captain Thorn. He was clearly Ellen Guon's invention and as such he is mentioned in some earlier series bible and is then referred to in several other places--including the Wing Commander III novelization, where Blair talks about a previously unknown period in which Tolwyn accused Thorn of cowardice and took command himself (presumably this is when Wing Commander Academy happened).
... but Wedge is correct that Halcyon refers to himself as the Tiger's Claw's commander at one point in The Secret Missions ('I'd rather not command a slagged ship', or somesuch). The timeline works out like this:
Captain Sansky commands the Tiger's Claw from an unknown point until the movie, where he kills himself. Commander Gerald, the next in the chain of command, takes over for Pilgrim Stars but is never actually promoted to captain or permanently assigned (the book actually makes a point of this). Captain Thorn is assigned to replace him. Commodore Tolwyn accuses Thorn and usurps command for Wing Commander Academy (and part if not most of Wing Commander I). He either moves on to greener pastures beforehand or simply decides not to accompany the carrier on the suicide mission against the Sivar--leaving Halcyon in command (the fate of Commander Nelson is anyone's guess). By the time the 'Claw returns to human space, Thorn has been cleared of any charges and returns to command for Secret Missions 2 (and probably the carrier's death the next year).
The Irish lady in the show reminds me of the mechanic from WC2, and many of the ship designs on both sides span from WC1 to WC3. Finally, it seems like Blair is shot down in almost EVERY episode (without being given the Golden Sun or the speech about how Confed's fighters are expensive, etc.). I loved the show (infinitely more than the movie), but these inconsistencies and anachronisms threw me off too.
The 'Irish lady' was a different character--her name was Maya McEdance. The mechanic from Wing Commander 2 was Janet "Sparks" McCullough--although she was certainly still around in 2654 (she shows up on the Austin the next year in Freedom Flight). Any similarity there is probably actually a coincidence... Wing Commander Academy's cast was derived from the Victory crew in Wing Commander III (*all* the same pilots, in the initial plans). Maya being distinctly Irish was likely to make sure we know she's *not* porn star Ginger Lynn.
(And her Scotch-Irish American last name aside, Sparks isn't Irish in any way in the first place... she doesn't have the early games' /charming/ accent-in-text like Paladin and on the rare occcasion that you hear her voice she's as Texan as anyone else in Wing Commander II...)
I think the ships are all specifically ones that don't have a known entry dates--that's why we're seeing Scimitars and Grikaths, which the existing continuity said can be around at the time, instead of Morningstars and Rapier IIs which we specifically know when they entered service.
I think Blair ejecting doesn't happen nearly as much as you're thinking, but it's really the problem with Wing Commander as a setting for a show. Academy decided to go 'straight' and have the pilots actually be fighter pilots... FOX's Wing Commander-with-the-numbers-rubbed-off show, Space Above and Beyond, had to invent an elaborate and nonsensical background about how the elite fighter pilots were also ground troops. I like Academy better, but it did mean they had to come up with reason after reason to put the characters anywhere interesting.
(Correct me if I'm wrong, though, but did Blair actually eject only once? The show got that reputation because the episode where he ditches and the episode where he ejects were run one after the other...)
Red & Blue - Nothing.
The Last One Left - Surrenders to Karnes, fighter survives.
The Most Delicate Instrument - Nothing.
Word of Honor - Ditches, fighter survives.
Lords of the Sky - Ejects!
Chain of Commander - Nothing.
Expendable - Nothing.
Walking Wounded - Nothing.
Recreation - Nothing.
Invisible Enemy - Nothing.
The Price of Victory - Crash lands on the ice planet, fighter destroyed but he doesn't eject.
Glory of Sivar - Crash lands a Sartha--on purpose as part of the covert operation.
The silly bit about the Golden Sun and the speech aside (we don't see it! it must not have happened!), that brings to mind an interesting question--canonically speaking, when *did* Blair earn his medal? Discuss amongst yourself.
I know the Rapier is a different craft in the movie than in the game, but isn't the movie Broadsword supposed to be the same craft as the game Broadsword, just re-imagined?
Never understood why...you went to all the trouble to make the two Rapiers be separate; why not make the two Broadswords separate as well? But that's what I've heard.
I think because it would just seem so increasingly improbable--if you can accept that the actors/sets/etc. all look different, the ships seem natural. Insisting on a backstory where that's somehow a different Tiger's Claw around at the same time with the same people on it and a different set of fighters that all have the same names... it would satisfy some incredibly crazy geeks but lose any versimilitude at a much faster rate.