The Master Dungeons are a result of my efforts to focus the DCC line and keep it true to the original vision.
DCCs are very specific: They are sword & sorcery crawls. The NPCs all die by the end, there better be some secret doors and death traps, and if a PC doesn't die somewhere it was because the GM was soft. DCCs are REH, Leiber --- golden age pulp material. Gritty, bloody, and a lot of fun. (Consequently, due to the confining parameters of a "crawl" they are pretty easy to run, but this is a result of the design, not the intent.)
In contrast, Master Dungeons are more open. They are epic in tone (though not necessarily levels, ala the Heroic/Paragon/Epic tiers). They are less street level gritty (which I love) and instead high fantasy. The NPCs might not die --- in fact you might want to talk to one or two of them (and kill them afterwards

). PCs are assumed to play a crucial role in campaign setting --- whereas DCC heroes can quite easily be wandering homeless people with weapons, the default for MD heroes is that they are the champions of their realms. The stakes are higher, the stage is grander, the consequences are dramatic. If the PCs fail, it's not just their lives that hang in the balance.
(Note that this is just
default assumption. DCC heroes can be regents and heirs, and MD heroes can be wandering vagabonds, but the assumptions leading into the adventure have a different flavor.)
MD allows a writer a bit broader scope. Consequently they can be a bit more challenging to run as a GM. While the plot is jsut as clear, and the goals are understood, PCs have more options on how to meet the challenges.
If we were talking classic Mentzer D&D, DCCs fall under the Basic and Expert sets. Master Dungeons are Companion and Masters. The quality of play isn't different (neither one is "better") but the tone and themes are.
Wow, very cool. Interestingly enough, my campaign forked into two groups that each match one of these categories. It'll be fun seeing what modules are released for each line.