How can I make Shepherd's Pie without tomatoes?
The tomato in shepards pie provides acid and is the main coloring agent of the meat portion of the dish. Any other acid will work in place of it, although which you use will entirely depend on how much you want the flavor profile to stay the same.  Adding lemon juice will give your pie a Mediterranean taste, adding others will result in other flavors coming to mind.  You could just leave the tomatoes out and use a roux instead of the flour, that should give you about the same mouth feel just tasting onions and lamb.