Both of the games have teh same basic mechanics, but the number of cards planned per turn is different which gives a distinctly different feel to each game. WWI was more about the pilots and their personalities, while WWII was mostly about the planes... and this comes out as a "feeling" in the games as well.
The big thing to keep in mind is that the WWI version has a lot more material out for it which gives a lot more options for missions and game play. I personally like the WWI version better, even though I like WWII planes better. If you are a miniatures player, there is no choice but to go with WWI now. It has more then twice the number of minis out as WWII does.
You should check out the site Wings of War Aerodrome, it is the fastest growing and most active site for this game out there.