Yes, the arachnid thing was annoying as hell. But the other day I picked up my GBA and started playing Fusion again, and beat it third try. My other play throughs, it always took me forever. The SA-X, which I thought was hard, turned out to be pretty easy this time, and I actually beat the game.
I probably have already answered before, back when I was active in the forums, but I'll do it again. The hardest boss I've fought is probably Sephiroth from Kingdom Hearts.