Neither is very hard. I would say the Hades battle in general is harder because of the cheats. No traps on Poseidon plus the bigger hits and healing cheats. Morganthe barely cheats at all.
I would have to say it depends on your team for me. If you have a good feint stacking team and a storm 2 Morganthe runs can be finished very easily. While a good storm offensive team with one or two jades, (depending) can easily beat Hades.
I would love to be able to answer this but am still in the beginning of khrysalis part 2... I started when it first came out but questing alone can be boring so I just stopped /:
Hades is much harder. Morganthe is just four 26k health bosses. Whoop dee do. Hades has annoying cheats, especially mr you can't trap me Poseidon. Try doing Tartarus with a storm hitter without shadow.