Now, this is all theory, but as stated by RadioRebel in this forum,
"Suicune was used as the mascot because the thing on its head is shaped like a crystal. Crystals, particularly rare gemstones, fit in with the Gold and Silver pattern. Granted, they could have gone with Ruby for Entei or... some yellow mineral for Raikou based on color alone (or anything else really, Ho-Oh and Lugia are red and white, and Giratina is purple, so the names don't always have to fit), but the fact that Suicune actually had something resembling a rare mineral on it made it the obvious choice."
Kinda makes sense, right?