One of the things I've always loved about WC is the right mix of story and action it brings to the table.
I remember playing Half-Life for the first time and thinking, what a great game, and a good story for a FPS. Looking back on it though, I spent a long long time just making my way through levels, shooting endless bad guys and seeing something humorous or of storyline signifigance every once in a while. Looking back on the story itself, it's not that complex, doesn't have any appreciable character developement, and the only thing that made it 'deep' was the fact that most of the time the player was oblivious of what went on 'behind the scenes'. Hopefully HL2 expands upon this, and i'm sure it will. I had a great blast on HL and still consider it the best FPS I've ever played.
I have similar feelings about Halo.
Wing Commander though...The characters were 'real'. They had motivations, attitudes, quirks, and even families. The characters were developed and 'believable'. The story, though not a new concept by any means was well-developed and had a certain unique feel to an often done scenario. Even the enemies were cool. Thrakhath was a formidable enemy indeed and the player (or at least me) was chomping at the bit to finally settle the score after all we'd been through.
Wing Commander wasn't always "One man to save the Universe" (of course there was a bit of this but it was needed I think). You had wingmen, you had crewmates, you had a carrier that for the moment you called your home. You suited up, hopped into the cockpit, and flew out to save a destroyer, some other pilot's temporary home.
There was politics, and the player often had their own opinion about what the politicians should be doing with our hard-earned cred.
The enemy had their own politics and motivations as well. Wing Commander had it's own universe. Background, motivation, a theme. Confed had their backs against the wall and all a man could do was promise himself that he would fight the good fight.
After the war, new problems arrose out of the ashes of Kilrah. Peacetime budget concerns, recession, the need for a strong military on the scales against the need for a balanced budget...
Wing Commander had the depth and feeling that so many games lack these days.
Maybe it's because of a change in the industry? Game manufacturers are no longer a small group of collegues and coworkers who want to bring a vision to life and share it with the world. No longer storytellers, who instead of writing pages, write code.
Instead you have the corporate world of gaming. It's not about making a great game to make a great game. It's about making a great game for the aim of making money. Of course this is and always has been a motivation, but it is more mechanical than ever. If first person shooters are what's selling, first person shooters are what you get.