Tolwyn's flag was on the Austin during part of WC1, according to Super Wing Commander.
The TCS Concordia (CVS-65) did not come on line until 2661 (Fleet Action) -- the Confederation class itself, because of the fact that it is based around the PTC recovered from the wreck of the Sivar and the fact that it takes five years to produce a carrier, could not have entered service in 2660. Thus, the TCS Concordia referenced in the transfer orders for Downtown, Shadow et al. in the Kilrathi Saga manual is the Concordia SuperCruiser! Presumably, the supercruiser was destroyed at some point between 2657 and 2661 -- and the name was re-used for the Confederation class ship (it fits with the naming convention, and it would seem to be tradition to always have a Concordia in service).
Timelinewise, the movie takes place several months before Wing Commander 1 -- almost immediately after the first episode of Wing Commander Academy.
The fighters do, indeed, have shields -- you can find their specifics in the Confederation Handbook if you're interested in seeing how they match up to the other craft of the era. As in any movie (WC cut-scenes included), combat must be much quicker in FMV to be entertaining. You do, indeed, see the shield glimmer during the combat in the movie, though... (except in the case of the enemy battleships, which had taken down their shields to fire their torpedoes).
Paladin has, apparently, *always* been a spy -- even when he was a pilot. Angel and Blair being attracted to eachother is not necessarily anything new in WC2...