Via plating thickness will affect electrical and thermal resistance of that via, which may be important depending on your application. Here is a handy calculator for determining via electrical and thermal resistance as a function of hole dia, plating thickness, and via length: http://circuitcalculator.com/wordpress/2006/03/12/pcb-via-calculator
I would check with your board house or CM to determine which standard plating thicknesses they offer, then use the calculator to pick from amongst those.