If I had been asked this question two years ago, I would've probably answered Twilight without even considering The Host. It took me almost two years to read it - I started it in May 2008 when it was published and after over 100 pages I gave up trying. After that I've heard so many people say how it gets so much better when she's found and she's in the cave and finally now I started reading it. So I read the book and loved it.
Now that I ask this question, I'd have to say The Host. Twilight made me first fall in love with Edward and then Jacob and I was hooked since page 1. With The Host it took me over a hundred pages to get myself hooked. If that was the definition for which book I liked better, then it'd be Twilight. But I don't define it like that. For me the better book is the one that makes me feel for the characters, identify myself with them and make my laugh and cry. And when I think that, I really can't identify myself that much with over 100-year-old vampires who are perfect and glittering. And Bella... well, I sort of could relate to her when I was a teen myself but now - as horrifying as this may sound, even to me - Twilight has sort of lost its spark. I love happy endings but after Breaking Dawn I found Saga's ending TOO happy.
I loved The Host because it had real humans in it and they acted like humans. Yes, it had aliens and they were kind of perfect too because they disliked violence and they were polite and didn't lie and etc. but that's not the same thing as it was with Twilight for me. The Host, too, had a happy ending but I really wanted it to end happy. I didn't know how it ends but when she thought she was dying I was so happy when I found out she didn't after all die. I'd fallen in love with Wanda and Ian and wanted them to have their happily-ever-after because they really deserved it after everything that had happened.
Also I liked the story line better with The Host than with Twilight. In Twilight Bella and Edward fall in love way too fast and everything happens too fast for me. In The Host Wanda of course loves Jared but that's at first because of Mel's memories. And I liked how Ian and Wanda started to become slowly from enemies to friends and not just:
Day 1. I hate you and want to kill you
Day 2. Friends?
Day 3. Marry me?
That was the reason I'm now not liking Twilight the way I used to like it. It all happened too fast and seems so unrealistic. Yes, I know, alien+human relationship seems a little unrealistic too, but if you take that out and think of Wanda as a human, too, then you get my point.
So I choose The Host(and now I have Edward's voice ringing in my head in Eclipse's tent scene

) because, although it took me longer to start liking the book, the way I liked it was much deeper than with Twilight, if that makes any sense.
I didn't mean to write this much but after I started I couldn't stop

Somewhere in the near future you will be looking my signature instead of this message.