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?
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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.