Not that I really think it's too much of a problem, I got used to it, but I do think I was tripped up by the down button being an *overhead* attack.
You're swinging the sword over your head onto the opponent, it's not typically described as "down" like you're saying. Though moving the overhead to the up button would force the thrust to be the down button, which probably isn't much better. It's just preference I suppose. Fun game nonetheless.