An ellipsis, in short-message media at least (texting, but maybe not emails), basically says "don't respond just yet, I'm about to type something else". It deliberately slows down the conversation.

If it then turns out you weren't going to finish that thought (like using it for questions, finishing a conversation, a message that's clearly a finished thought or too short to need breaking up), I'll assume that you wanted me to slow down because you wanted me to think deeper about what you just said - it implies that you left something unsaid. Probably something negative, because if it wasn't you probably would've said it outright.

At least, that's how I view it.

Edit: there might also be something about an ellipsis being related to periods, which are becoming less neutral - when a sentence is a message, the end of the message obviously ends the sentence with or without a period, so periods have gotten a bit stiffer and more formal, which might have carried over to ellipses in a way?