I can see an alternative. It consists of 2 adjustments:
1. Reloading missiles of the same type should not cost a turn. Currently, when you equip a stack of identical arrows, this means that whenever you fired a shot, your next arrow is instantly ready to fire. Why would a slightly different arrow not be, then? It makes no sense..
When you run out of arrows, reloading a new stack of arrows should be instantaneous to be consistent.
2. If 1. is done, then all that's needed is a setting where you will reload missiles automatically, without any prompt.
Ideally, this should only work for missiles that are identical except for their to-hit and damage modifiers. That way, you can have variety in missiles, but be able to use them as if they were a single stack. And without worrying that you might accidentally waste your valuable arrows of penetration on a kobold, etc.
An additional advantage would be that this would also work when you're throwing daggers, spears or whatever.
[Edit] or the quickmark method could be used that Adom-Admin proposed in another thread. Would come down to more or less the same thing, only read that post just now. [/Edit]
If all that is too difficult to implement, I vote in favour of removing missile variety.