There's no way those magic dart are a better use of your time and resources than another shot of summon ice beast or whatever, but you have to do it anyway. It doesn't take skill. You don't have to think about it. It isn't more "realistic." It adds nothing of value to the game. It's just a big waste of time for no reason.
Well, I think that maybe this is where trainers come in. The player can spend money, which he can acquire through the use of any skills he likes, to boost a completely different skill. I would argue that while this method of skill advancement is far from being completely realistic, it may be a least somewhat more realistic than the system that crawl now uses. And that it what makes such as system attractive to me.
Someone already alluded to this, I think, but if the player thinks the most entertaining and useful way to allocate their time is to mindlessly perform repeated actions, it may be that there are other problems with the game's design besides the way skills are advanced. Ideally, players should be able to advance their skills through repeated use while also participating in the story or doing something that feels meaningful and in character.
And let me be clear, it sounds like crawl came up with a very creative and highly functional solution to the issues that we are dealing with here. I just like games that, at least in part, allow skills to advance through their repeated use.