The motivation comes from topology.  Suppose you have a map of topological spaces f:X --> Y.  You want to form the homotopical version of Y/X, so instead of identifying X to a point immediately, you do so gradually, so you form Y union_f CX, where X is the cone on X, and you glue the base of the cone to Y by the map f.

So from the point of view of the cells, the cells of the mapping cone on f in dimension n are

the cells of Y in dimension n

the cells of X in dimension n-1 (cross the 1-cell in the cone direction).  

To do this with cochain complexes, you ought to form 
 
Y in degree n

direct sum

X in degree n+1 (because you're using cochain, not chain)

The differential also comes from the topological motivation.