It's not as if Lugia is the only Pokemon with traits that differ from the games... Look at the DP-on Seels' weaknesses. ;p Odds are that certain mistakes were made early on in the games that couldn't be corrected. Though Lugia could just be a case of "It should really be 3 types, but we can only make it 2". The TCG is a lot easier to "update". Changing types on things doesn't break the game here as it would in the games. There's a reason only 2 (well, 3 if you count the alt. Rotom forms) have ever changed type. And even then, two only added one.