Also, here is another awesome essay entitled Why Neal Had to Die.
Because if you want to stop talking about a crime, you have three options: address the crime, kill the villain, or kill the victim.
Neal had to die to cover up Hook’s misdeeds, thereby enabling his character to be whitewashed as a “romantic hero” without him ever having to come clean to Emma about what he (and Milha) did to Baelfire in the past. Also, with Neal out of the picture, the audience can conveniently forget that Hook is not only a potential step-dad to Henry, but also was to Neal (and was a horrible father figure and friend to him). Whether or not you liked Neal isn’t the question being asked, as this other essay writer replies. Killing Neal had to take place to make Hook look better. It also had the added bonus of taking away Emma’s choice (since Neal was after all confirmed as her true love).
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy