They're typically the worst "dungeons" in the game in the 3D Games. Pretty much all of the 3D Zeldas end on a really lackluster final "dungeon" (Ganon's Castle in OoT, Ganon's Tower in WW, Hyrule Castle in TP). Sky Keep in Twilight Princess was really good, though.
Yeah, IMO none of the 3D Zelda's final dungeons can hold a candle to Ganon's Tower in LttP. Though, Sky Keep was pretty good.