I'd like to imagine that the beacons were a Prothean creation. In my mind, they are the true heros of the Mass Effect and their tale is so tragic. Come on, give 'em something.
Well, I'd like to think that their worth comes from the fact that sapient species are unpredictable in ways even the Reapers in all their knowledge couldn't imagine, so in a way it's better if they have their own technology work against them. That's why the theory of Protheans and Humans being more closely related makes sense. Well that, and because it also ties neatly into these depiction of the other alien species developing at a slower rate than humans (even when being more advanced), and how mankind is so diverse and driven and they have space jesus and everything and why the Reapers find them so appealing and useful.