This is something I’ve had a really hard time doing. I get so emotionally involved with my characters that I base the whole story around what’s best for them, at the expense of everything.
For the first time recently I’ve been trying to figure out the plot and what would be most interesting without thinking about which character I like the best.
I find myself most interested in writing fantasy/scifi/paranormal-romances. Mostly because i can make up the rules and max out my imagination while making people fall hopelessly in love. But these genres often include a lot of battles and I have never wanted to kill off someone I really actually liked.
No more.
If someone needs to die to move along the plot, I will do it (as long as it’s not my major protagonist/antagonist) … because then the story would be over. 🙂
I think what I’m trying to say is detach yourself from the emotional aspects of your own story. You will probably be able to write better and with a plan, you’ll know ahead of time what needs to go down in order for your story to be the most successful.
A series that really embraces this idea is Game of Thrones (I’m on book two, but so many people have died already). George R.R. Martin has no issues screwing characters over, killing them, putting them threw the ringer and in general making all their lives so miserable that at times you feel bad for all of them. I don’t think I’m quite interested in going this far, but in taking his lead I’ve learned that strife can increase the intrigue and evoke more emotion in your reader than only giving them the sweet and sappy.
So, in conclusion, don’t be afraid to smack your characters in the face.
E.E.
Endless Edits 
Sometimes the only reason you have a character is so that they can die. No matter how much you as the writer may like that character they are there to drive the plot. Ned Stark is a classic example. You can have as many interesting characters as you like but without a well planned plot it’s fairly meaningless.