Honestly, for me most of the micromanagement in the X1 airgame was selecting/deselecting missiles and cannons to make sure I wasn't wasting torpedoes on fighters, or shooting all my small missiles at battleships.
I'm not sure of a solution beyond being able to set engagement parameters such as 'fire x-type weapon at y-type target' as a sort of standing orders or common sense for your pilots. Of course, you can countermand the orders, but that's your choice as the commander and not constantly clicking and clicking and clicking in every engagement.
Or maybe just getting rid of missiles entirely like XCOM did in the mid to late airgame and using laser cannons and railguns that don't have arbitrary short ranges?