When Kube reaches much later stages in development, do you imagine there will be a small preferences section, which doesn't extend too long:

It might for instance allow simple things like:
-Most recent message at top of thread. Kube's default is they go at the bottom. (Y/N?)
-Hide/show most recent messages [sent messages are now collapsed via default unless you click 'show')
-Reply above/below the quote? Roundcube has this.

Whilst you have said that you want to keep the client streamlined, there should be some limited 'preference' for users.