As a programmer who deals with wordpress on a daily basis I feel like I have a different view to it's inner workings. The simple functions for the_loop(), the_title(), and the_content() are things i rarely touch, as they are more template functions for displaying templates. There is a reply to The post that describes using "do_action" which depending on what you want would be a better option for achieving the formatted post content.
However, I have a real love/hate relationship with wordpress plugins. Writing plugins is very easy, and there is sufficient documentation within wordpress itself to describe most functions. However, there are a LOT of plugins I've come across that are written terribly. I would love to express my dislike of them, however I've taken on the "If you cant write better, then don't criticize" mentality.
Maybe one day I'll feel confident enough in my skills as a coder to name and shame these scripts, but for now I'm concentrating on becoming a better developer, and writing good PHP.
I agree that the Loop can be convenient at times. But I still contend it's bad architecture--just as many seemingly convenient programming practices are.
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.