Maverick didn't meet Maniac on the Tigers Claw,
You've lost me on this one -- Blair meets Maniac at the Academy in the movie, the TV show and in the games...
the Tigers Claw is a submarine,
Assuming we're not addressing this literally, how is this any different from changing the look of the 'Claw for Wing Commander Academy or for Super Wing Commander (or, for that matter, between the beginning and end of Wing Commander 1 itself -- count the engines)?
I'll tell you how it's different: you're not digging for excuses to discredit any of these other sources.
the kilrathi are stupid enough to be unable to distinguish between an annomoly in space and a terran fleet,
Ignoring the Confed Handbooks more obvious explanation (which I believe, but also find silly), the nature of things like quasars (specifically, quasars) is that they put out a lot of radio signals. Scientists on Earth have been tricked by exactly that before -- thinking that the emissions of a quasar are intelligent signals.
they're also green and rubbery
The Kilrathi are not green (they're brown) -- they're in a green atmosphere. They are no more or less rubbery than the rubber Kilrathi in WC3 or 4.
, skipper missiles are introduced far too early,
A matter of semantics -- neither the movie nor WC3 state that Skippers do not exist already. Eisen claims that the Kilrathi are testing "a new
type of cloaked missile". It would make sense for cloaked missiles (especially larger ones like in the movie) to exist *before* cloaked fighters, no?
there was a war with an offshoot of the human race known as the pilgrims,
Oh, well, I'm *sure* that in the 600 years of completely undocumented history between now and WC1 in the WC universe that makind *never* fought amongst itself over *anything*. Note: sarcasm.
the kilrathi getting to earth is not a matter of the number of jumps or getting passed defences but simply of a navcom AI,
The Navcom AI, plus capture of the Dakota System where exists an unusual jump to Earth...
I'm... not sure you're right about that...
And what does this contradict with? What was Blair's stated religion *before* the movie came out?
There are plenty of legitimate complaints about the WC movie. These aren't them.