Synthetic life was a necessary sacrifice. Regrettable, but necessary.
The natural order is of paramount importance in my eyes, and the Reapers are abominations. Killing them was a mercy.
Anyway, it mattered to me.
As for DX:HR, what endings do people tend to pick? Afaik, the vast majority pick Sarif, and one of my "friends" picked Taggart because he genuinely believed he was right!
To enjoy the Zelda games, you really need to get comfortable with the central themes and general layout. Only then will you be ready to play Majora's Mask and wonder why it's just so dark and unsettling. Twilight Princess is pretty weird too, so you should start with the original, then do ALttP, then OoT. They should give you a good footing in the universe. Bear in mind that my personal favourite Zelda titles are :
1 : Majora's Mask,
2 : Oracle of Ages/Seasons,
3 : Twilight Princess/Link's Awakening,