MM did a few things better than OoT did. yes the time travel mechanics could have been implemented better. and yes the main villain was random but i don't think he was weak. the skull kid was a very memorable and liked npc's from OoT and seeing him being controlled like that made things a bit more personal. seeing him wreck havoc upon the land and its people made it so we get more invested in the story. and the fact that the npc's interact more with you in this game makes the world feel more alive to me.
yes i did enjoy having a darker side to the game. the game is oozing with melancholy and depression. almost makes you wonder if the game devs were feeling down when making the game. they manage to convey that feeling quite well. i dont think they chose to make it dark just for the sake of it but rather using it to better set a tone that enhances the doom and gloom atmosphere.
for the record, i loved OoT and even both WW and TP. but the latter two games had some pretty big flaws that takes away from the experience for me.