Oh, good, another canon discussion.
I'll be the first to admit that I'm not as hardcore a WC fan as some of the long-timers on this site, and while I've been coming here sporadically since the site's inception, I've only started taking active part in the disussions recently. But I've been in love with Wing Commander since I first strapped myself into my Hornet cockpit with Spirit on my wing, oh, probably fourteen years ago. So perhaps my opinion represents a nice middle ground of fandom.
I see the thoughts behind both sides of the canon discussion. On one hand, I myself have struggled with many of the apparent inconsistencies of the franchise. The problem with the franchise is that, to someone who hasn't read the strategy guides or the novels, or perhaps never had the opportunity to see Academy or play Armada, there are a lot of apparent inconsistencies, especially between the movie and the games. This is because the games IMPLY one thing, that is often in contradiction with other things, or make a statement that, taken only within the context of the game, indicates one thing that is at odds with others. A good example of this is the recent discussion about Maniac's and Blair's first meeting. In WC1 Maniac greets Blair with a "Please to meet you!" with no other context about his background aside from the Claw Marks manual, which says nothing about him knowing Bluehair. Normally, when someone says "pleased to meet you" to someone else, this strongly implies that they are meeting them for the first time, unless there is obvious context that they are saying it ironically. However, that context is absent in the game, and it is only apparent after reading the strategy guide or watching Academy (neither of which I have unfortunately had the opportunity to do). There are many other examples...people familiar with WC1 know Bossman dies during the Sivar Eshrad (sp?) incident, yet the movie states that Bossman died before Blair joined the Tiger's Claw. In the canon, Bossman was not really dead at that point, only captured or something (I understand from LOAF, although how he managed to get captured and his fighter somehow made it back intact to the Tiger's Claw I still need explained), but there is no context in either the game or the movie to clarify this...so it's a glaring contradiction to people who have only played the game and seen the movie. A third example is the Pilgrim wars...the movie implies that these were a major, major event in Terran history, with a lot of lingering prejudice and ill will, and yet they are never, ever mentioned directly or implied at indirectly (unless you count distrust of Border Worlders in WC4...but I thought the Border Worlders and the Pilgrims were distinct) in the span of six whole games. I think such contradictions are what the original poster is driving at, and I can certainly see his point of view. Remember, hardcore fans, what the universe looks like to those of us who haven't read (or helped to write) every scrap of material that is out there...
On the other hand, it's important for people who complain about continuity to remember that EVERY francise will have continuity difficulties, especially if you look at only some of the pieces. This is inevitable when you have more than one person working on a project--each person has their own ideas and will add their own elements, and often communication is not perfect enough to make everythign mesh perfectly and imply everything else correctly all the time. It becomes even more true when your sources are all on different media--games, novels, strategy guides, game fiction, movie, TV--with completely different production crews. Even if you had a person, or a team of people, overseeing continutity of everything, there is simply too much for them to catch everything. I think one of LOAF's major points is that this is exactly why the concept of canon even exists...so that subsequent developers of both fan-driven and official projects can fit what has been established and keep future continutiy errrors as small as possible. For example, both the movie and the games involve Bossman. A canon describing his life...why he wasn't on the Claw when Blair first arrived, what his family was like, and when and how he actually died, etc,...has been established that fits the different pieces from the game, game ficiton, and movies together. If some future game or novel or movie revolving around Bossman's life is made (which would be cool in my opinion), then this canon is very useful in making sure that this new product DOESN'T contradict what is already known, which may be why LOAF and others are so set against having multiple layers of canon.
Incidentally, it does seem that every franchise has continuity issues, and it would seem that Wing Commander is better than most in not contradicting itself, once one gets deeper into the fiction. Far better than Star Trek, Star Wars, etc. (in fact, the only sci-fi franchise of similar magnitude that has better continuity that I can think of is Babylon 5, but maybe that's cheating because it's mainly a TV show and a series of movies and novelizations...there were never games or independent novels). For that matter, it probably has tighter continuity even than Lord of the Rings, which WAS created by a single person.