I think the size is an uphill thing for Bogaerts - but he showed enough the last year and change for scouts to have changed their tune from "surefire 3B" to "yeah, he could stay at SS for a while". That is the entire source of the hype.
Middlebrooks will never be an on-base machine. But he also is a superior athlete to say, Napoli, and could offer a lot more in terms of defense and versatility. He showed he could at least fake 2B, and I'd have no problem giving an athlete of his caliber turns in a corner OF position. If he concentrates on becoming a really good defensive 3B (which he isn't yet, but clearly able to), the total package along with the raw power can make up for low OBPs. The comparison I always use is Josh Reddick. Reddick does so many good things that his OBP can be low but acceptable enough to access all the good stuff. Last couple of years, Reddick has been OBP enough to be a solid starter. Can Middlebrooks get to that level (which would still be below average)? I think he can.