Ashera from fire emblem was a beast; she virtually commited near genocide to thousands of humans and laguz, as well as lie to hundreds of people who survived, in which they believed that they were the 'chosen ones' and thus Ashera gave them holy-like weapons and armor. Fighting her? She's arguably the hardest Final Boss in the whole Fire Emblem franchise, with all good reason. First you'd have to break each one of her protective 'auras', other wise you won't be able to actually combat her. Even when you've destroyed the auras, there's another catch if you'd want to defeat her - you have to beat her with only the weapons that were 'blessed', which you'll be able to have your weapons blessed at an earlier part of the final chapter, but, yes, it's the only way to harm her or else you won't deal any damage.
I loved Hades from Kid Icarus Uprising; so witty and hilarious! Playing against him is a different story though. He's actually a really tough final boss if you've played him on the highest difficulty, what with his purple lasers of DEATH and his blue blobs of DESTRUCTION, but he's fun to try and beat anyhow!
Dahlia Hearthrone? She was probably one of the most dangerous characters in the Phoenix Wright series: killing off various people one after another like her older sister and Terry Fawles (well, basically she tricked him in committing suicide) just for them to keep quiet about the 'false kidnapping' to steal a priceless gen when she was just 14, as well as Doug Swallow to keep quiet about her, almost killing Phoenix too in the same episode, and she almost killed off Godot after her trial ended that same day.. she tried to kill Maya Fey, and aaaah, so much bloodlust in her, as she tries to masquerade it in this "cute persona" of hers.
Junko Enoshima is practically insane! Traps students in their own schools/islands, wiping their memory clean, causing them to kill each other all for the sake of bringing despair in the world?
Who does that? Plus she always takes on different personas in a conversation; like she can be a badass in one, a sort of 'teacher' in another, and have this sorta cute persona in another.. she's really unpredictable.