I get what you are saying, but the setups are entirely different. DMD is a father-daughter thing. No backstory is needed to explain why two such people might come together and spend a lot of time in each other's company. All the backstory that is given can easily be centered around just these two characters. The side characters then end up being people one or the other know, and get introduced to us over time as we have reason to meet/see them again.
With Melody the point is this is some complete random stranger. Could Mr. Dots have simply jumped in with, "Hey, you teach music to young adults and here's your newest student... begin," yeah, he could have. It would have created need for flashbacks and such to keep some of his plot points the same and intact, but it could have been done (although flashbacks aren't the best tool in games like these). He also could have edited some of the plot in ways that made some of the backstory unnecessary. I too prefer a game that gets to the core faster, but the story he chose to go with does kind of require the long-winded intro.
Either way, once past the introduction you've pretty much got all your main and side characters in the game. Moving on from there is pretty much just time spent with one or another of those already introduced. It isn't like every release is 3 new characters. So pacing does clean itself up a decent amount.
DMD is a game that plays out more like there is 1 central couple and then several bit players that continually poke their head in from time to time. Melody has more of a feel like you aren't really sure who the main couple is, or that you have a choice in the matter (for good or bad). Since Melody is the title character though, she seems to get all the game mechanics pointing to her and splitting screen time even when other characters get more/better scenes.
Intro aside, the central theme of naive girl corrupted (by someone in authority over her), the quality and style of graphic artistry, not to mention the general style of the writing is all the same in DMD and Melody. There are plenty of differences between the two games as well, but it is those 3 (well, plus the obvious "coincidence" that they are made by the same author) that causes all the comparisons. Melody is the more convoluted game from both a story and mechanics point of view (for better or worse).