The only boss in OoE that I really do hate is the giant crab thing that chases you up the tower. I have no idea what they were thinking on that one. Every other boss in OoE is completely fine, in my opinion.
I think SotN is maybe a little overrated! I mean, it's still great, but I played it after most of the GBA/DS Castlevanias and it does nothing to really wow me.