As for enemies yeah a lot have yet to be brought to life into the 3D world including the Lynel, Goriya, Darknut, Lanmola, Patra, Pols Voice, Vire, Zol, Daira, Doomknocker, Fokka (bird knights) and basically almost every enemy from AoL.
But OoT did bring back the Lizalfos from Zelda 2.