I know they're both polite ways to use a verb, but my materials never taught me what unique traits each one has. Is it just the tone, or is there more to it?
お…になる sounds more respectful than …れる to me. In particular, when used to ask for the listener to do something in speech (for example at a restaurant), こちらでお待ちになってください is fine, but こちらで待たれてください sounds impolite (not respectful enough) to me. I do not know whether this difference is counted as “just the tone” or not.