(Not finished, playing multiplayer to bump up my galactic readiness)
The way they've made me care for these characters. I've cried so much throughout this game. I mean, if killing my favourite characters wasn't enough, they have to add the freaking BEAUTIFUL voice acting. I mean, all of the voice acting was so fucking perfect.
The crew interactions with one another is AWESOME! I hope other game companies take a page for Bioware, because I for one love listening to my crew talk with each other. Garrus and Joker telling each other jokes, Garrus and James one uping each other, everyone with Liara. It's the little things like that, that make the game real to me.
The Thessia after math. Especially with everyone being concerned for Liara, and then Joker being all "Anderson fucking told me to take care of you!" to Shep, that dialogue exchange was wonderful.
Jack. All of her. I loved her before, but she's in my top 5 favourite characters list now.
I love this game. Even if the ending sucks, I like to think that everything else in this game balances it out. Yes, I will be pissed if the ending sucks, but it's the little things that soften the blow.