Any ideas on how to accomplish this other than through scripting? When you run out of the current arrow type the weakest available arrows are automatically equipped but I'd like it to be the other way around. I haven't found any settings in the CK which controls this behavior.

I'm not sure it's always the weakest. When my character runs out of glass/dwemer/ebony arrows he almost always equips iron arrows, despite the fact that I always have a ton of weaker ancient nord arrows on me.

It is probably possible one day, but for the moment no.
Example: SKSE has extended the Weapon Script with functions to get Base Damage.

There is probably a work-around, if your willing to parse every mod that contains new Ammo to generate CSV file (Probably best to do the Top-10 Ammo Mods that are popular)
Format: EDID;FormID;Damage

And parse the CSV file to generate GetFormFromFile(FormID,PluginName) as Ammo

Its really a complex step, not sure if i have time to explain or come up with a sample module atm

I was going to suggest somehow using the name of the projectiles they are associated with.

For example, Draugr Arrows use "ArrowDraugrProjectile".