Game-wise, I always thought Lugia's Aeroblast was like one of the most boss things ever, and that gave me a real vibe that Lugia was something awesome. Ho-oh didn't have the same feeling, and I do prefer Lugia's more simplistic design.
The Power of One is really the icing on the cake, because it sets Lugia apart as something else, something with a caring understanding and makes it a truly unique legendary. What has Ho-oh had in the anime? A random sighting in the first episode, and then again in one of the last in the original series?
Lugia really resonates more with me, plus I got Silver because I liked it better way back when. Lugia it is for me.