Choosing depth of ceiling electrical boxes?
The number of wires in your box determines the size of the electrical box you need.  I personally find 1.5" boxes rather shallow for a fan install since you are often hiding some of the fan wires in the box - this is a bit brand dependent though.  

Also the depth of your box shouldn't effect insulation.  We are talking about the difference of an inch.  The insulation will have a little hump and will perform the same.