Yeah, I only bottom-reply when I know (or can reasonably expect, e.g. on a mailing list) that the recipient is using a mail client that's not entirely brain damaged. Otherwise, I'll either top-reply or (if I really do want to respond to things in-line) actually say "See below for responses in-line" to clue in the recipient that yes, there's actually content in this email.

But yeah, that's usually more an issue with the mail client (or perhaps the mail server if it's being exceptionally stupid and modifying emails before final delivery). Top-replies became the norm for some god-forsaken reason, and now clients treat the quote and everything below it as entirely optional to display.