The effects in both films were technically accomplished, but Gamera 3 has the edge from the effects scenes being better directed and more artistically accomplished. That may not be fair though, as GtB was aiming for a more intimate atmosphere than the grandeur of G3. Still, when I think back on both films it's shots from G3 that jump to mind first: the burning Gyaos plummeting to the streets, the fully grown Iris rising through the clouds to a moonlit sky, Gamera's spinning mid-air attack against Iris, and so on. The effects in G3 were so exciting and dramatic, and I think they have yet to be bested in the genre.
One thing I do love about GtB is the Zedus suit. While not a terribly original design, the suit itself was lovingly detailed and the suit actor had a convincing reptilian gait.
Argh, this thread has made me need to watch Gamera 3 again
