One of the thorns in my side regarding my love for Doctor Who has always been that whoever's in charge of these things won't just release a season-by-season series of DVD box sets for my collecting ease. Instead, they just put out sets of random stories from all over the show's long history.
I thought that Doctor Who: The Beginning might be a step towards correcting that trend, but it's probably not. And the clue to why may be right there in that set. The Beginning collects the earliest Doctor Who episodes, about half of the first season. It's got all the episodes of the first three story arcs, but when it gets to the fourth, "Marco Polo," it only has 30-minute condensed version and the explanation that the rest of the story is "lost."
Apparently, "Marco Polo" isn't the only story of the series to have missing pieces, and that would make a comprehensive, chronological collection difficult to produce for sure. Another story with lost episodes is "The Invasion," a Cybermen episode from Patrick Troughton's time as the Doctor during the show's sixth season. Two episodes are missing from the story, but what's cool about this one is that the soundtracks survived and the BBC has arranged for the episodes to be re-created as cartoons for DVD release.
It looks like I'm still going to have to collect the series haphazardly, but I love that the BBC is doing what it can to get even the lost stories out. You can see a teaser for the recreated episodes here.