The loop functions operate on (global) variables that are not explicitly passed into them. Therefore, without consulting their source, one cannot know what data they're touching. It's not obvious how and when these global variables get set and modified (which is one of the classic reasons global variables are considered Evil). Presumably, the variable are are set by the_loop(), but the opacity here is bad style.
On top of that, the fact that you must have these globals set to use the Loop's formatting functions makes it much less practical to use them in novel ways--i.e. in contexts other than the Loop. Sure, if you want that same data somewhere other than the Loop, there are other functions you can use. This is the typical reply I've heard in defense of the Loop. But that's a fairly poor defense: It's admitting that the API is so wonky, the WP devs had to create a bevy of functions that all do roughly the same thing to patch over each other's weaknesses. Why should there be a different way to get some post data in the main content area versus anywhere else?
BTW, I'm not just nit-picking Wordpress about the Loop. I'm talking about it because it's a well-known and very illustrative example of what I perceive to be a broader pattern of poor architecture throughout Wordpress.