But, in an MMO those systems all have to work together. The interrelatedness of things is part of what makes the MMO feel like an immersive world, as well as the important design principle of unity of subject matter. For example pets typically play a role in combat, and the player crafts items relevant to capturing (involves exploration), breeding, and/or training pets. Not to mention the problem of keeping the player's money balanced if they are somehow using the same money across multiple games. And if the money don't carry across, it would be quite difficult to make them seem like one integrated game. Making each of those playable on its own would make it more difficult to plug them into each other. So, I like the idea of modularity. I like your project breakdown except I'd toss out the necromancy and add a faction reputation/individual relationship meter instead, and a minigame arena or similar way to bring minigames into the MMO, and I'm fairly sure magic ought to be a sub-area of either combat or crafting, depending what you're doing with it. But I'm not sure this project breakdown works as a list of standalone games to be combined into an MMO.
The separate games wouldn't change how each system interacts. Say there's an mmo with a great crafting system but you hate the rest of the game. This would give you an option to experience the crafting without having to do the rest of the the stuff you dislike. Maybe off a smaller sub for that section of the game. Plus you wouldn't bring it all together at once. Maybe tie a couple together here and there, but you'd want to focus on the core game play before making it part of the game world. Smaller project chunks like this can allow you to have a sequel or two to fine tune stuff before pugging it into the collective game world. There's a lot of possiblilities on how to tie them all together.
All the games would need to be designed by the same team. You could hand off those designs to different teams, and as long as they meet your specifications, everything should work more or less OK.
I've mulled over this same thing many times. I love the idea of several smaller teams each making a unique game that would eventually be part of a larger game (be it mmo or not) but after awhile I came to the conclusion that there needs to be a "main team" that is in charge of the game, as a whole, that would stitch the pieces together and be in charge of making sure the pieces fit together in some kind of coherent way. I think as a single team though creating many small games as proving grounds for individual components of a future idealistic game is a great approach.
As far as modularity, however, It's unlikely to work well. Games, in general, are so entirely custom and even slight variations modify gameplay quite a bit. Look at shooters... you could say the gameplay aspect is modular there but each game has its own tweaks, stack, control flow, and many other aspects that make it 'feel' unique even though on the surface they may seem like the same game.