The boxed sets cost more than an individual release, which can made them tricky from a budgetary perspective, but they save the fan a good chunk of money when you look at the prices of individual DVDs. As far as the 2013 deadline, I think it's workable. I got to looking a while back, and there are 47 complete serials that haven't yet been given release dates (unless more dates have been announed since I first did this research a month or two ago). That means they'd need to release 12 in each of 2010, 2011, and 2012, and 11 in 2013. Well, in 2009, they released 17 stories to the R2 market, which is the market of first release. Granted, two of those (The Rescue and The Romans) were on one release, but still...12 a year is actually a slow-down in the release schedule! I'm not at all worried about the quality of the special features, and I like the idea of there being an "end" in sight.
I am disappointed that there won't be more animated fill-in episodes, though...it's unlikely many more lost episodes will ever be recovered, and animated substitutes are probably the best possible solution to the problem. Now even mostly-complete stories like The Ice Warriors will probably never get DVD releases.