Re: The Compose button:
I don't think there is an option to prevent the "action button" ("Compose") from disappearing, but I might be wrong. The intent here is that once you start scrolling, you don't need to compose.
Once you stopped scrolling, the button sometimes re-appears by itself, but sometimes you indeed need to scroll it up (or, I believe sometimes even slight movement down is sufficient).
I don't know what determines that. Kostya will probably address that in detail.
RE: The conversation view.
Kostya has written it in many responses (@Kostya: I was surprised it is still not in the FAQ): the conversation view is intentionally different from Gmail's. Aquamail is not a Gmail client with more options. It is a different app, with its own approach to many aspects of reading and sending e-mail. Many Aquamail users do not like Gmail's style of conversation.
I would recommend you trying Aquamail style for some time before you make any type of decision.