I've never been sold on the bottom-reply. Sure, if you're new to the thread it becomes easier to follow from the last, but if you're following from the first message it's a pain to scroll down to the bottom of every message to get what's new.
I would say I haven't seen an argument to convince me bottom-replys are better, but I honestly have never really discussed this with someone who cared.
Part of the etiquette of email, before gmail arrived and did everything for you, was that you elided irrelevant parts of email quotes. You don't leave the entire thread in situ; you only quote the parts of the message you are specifically respond to, or that are material to understanding the exchange.
The massive pile of shit problem is new to Outlook and Gmail.
Leaving the entire thread in was happening long before gmail.
So, bottom-first people are essentially don't-quote-irrelevant-crap people? In which case it would make sense to place the quote you're responding to above your response.
I would say I haven't seen an argument to convince me bottom-replys are better, but I honestly have never really discussed this with someone who cared.