I had a 2007 RSTD and put about 50,000 miles on it. I traded it in on my current 2012 Venture and it now has 20,000+ miles. I really don't think there is any difference in handling between the two. In my opinion, the stock windshields for both offered the same amount of protection.
They are are same bike beyond the stuff on the top side and I raised the rear of both with leveling links to improve the handling. In fact I had made my own leveling links for the '07 and then removed them to add to the '12 before I traded it in.
Storage is the big plus with the addition of the trunk for the Venture. You get the radio/cb with the Venture if that makes any difference to you.
After seeing all of the RSTD quick release windshields and sissy bar/luggage racks for sale on Ebay, with the RSTD I was always a little concerned about leaving the bike in motel parking lots overnight. Both items can be removed in seconds with the quick releases. I never had a problem - only a little concern they could turn up missing.
My '07 had the clutch whine and I really didn't mind it. I had the basket replaced under warranty but I don't recall that it helped much. My '12 does not have the whine.