Valid points, but...
In the movie, Paladin is flying the Diligent, a completely different ship. We've come to understand, that Paladin was transferred to Covert Ops by Tolwyn to investigate Pilgrim sabotage of the Confed war effort, hence his position at the start of the WC movie. The events of the movie and the subsequent tie-in novels occur, then WC1, at which point, Paladin returns to flight status, until he goes over to Covert Ops full time in SM2/Freedom Flight.
As for Blair coming to the Claw... Yes, yes, in WC1 it seems like he's meeting everyone for the first time. But this is more for the player than anything important to the storyline. In 1990, a first-time WC player had no idea who all these people were, and thus introductions were necessary. We have to remember, there was no Christopher Blair at this point. He had no identity or history. He was just "Player." He was you. It wasn't until WC3 that he became a real character. For all intents and purposes, in the movie Blair is seen going to the Claw after his graduation from the Academy. It's just that the events of WC1 don't occur until a few months later.
Concerning his relationship with Angel. It's clear the seeds of their romance began here, but didn't develop as the Vega compaign began to take a toll on everyone. It strengthens their relationship in WC2, I think, that they had a past together.
Skipper missile: As has been explained many times before, the Skipper seen in the movie is different than the Skipper seen in WC3, the WC3 variety being an upgrade. Hence, Eisen's dialogue: "The Kilrathi are using a new type of cloaked missile." As LOAF says, this seems to suggest there was an old type.