The HTML isn't particularly bad, it's pretty semantic. Perhaps it suffers a little from "divitis" but that is so that every element can be styled, it allows for much more flexibility in theming.
I don't see much in the way of inline CSS, though some plugins may add more. Most of my plugins actually give you the option to have CSS inline or let you put it in your Q2A CSS file.
As for SEO, actually it will hardly make a difference. There is no direct benefit for having neater code. Page speed is a fairly small factor, and Q2A still loads very fast on the front end so I think there is no chance of it affecting SEO.