The success of Minecraft severely damaged its development. When minecraft went viral and became a cash-cow, Notch decided to make Mojang into an honest-to-goodness software company. Mojang would make less money from rapidly improving Minecraft than from creating new products and selling them to new markets--markets which are augmented by the existing Minecraft fanbase.
The community would've done Notch's work for him if he let them. He could have started shifting the development of Minecraft to a model where the base game is a sandbox into which content makers can plug in different kinds of mechanics. But Notch didn't do this, he implemented a few nice, bigger features (like biomes) and a lot of piddly stuff (like more flowers, dyes, and such). Contrast Minecraft's content level with Terraria's: Terraria has been public a small fraction of the time, yet is continually adding new content and significant outstrips Minecraft in most meaningful measures of content.
Here's an example of where business gets in the way of game design and fun when it could have just as easily stayed out of the way. Here's where what is short-sightedly best for a company is not what's best for a game.
It also highlights the fading "games as platforms" trend. Notch could've turned Minecraft into a great platform for mods, but instead he has spent a significant amount of time implementing features that could've been designed and implemented better through the work of the modding community. The Minecraft community is large and the number of modders doing great work suiting the game towards different playstyles continues to grow. People have done all this work before Minecraft even had a real modding suite--these people had no sanctioned tools for modding, yet they did work of higher design quality and with fewer bugs and issues than the new content implemented by Notch himself. Imagine what they could do if they were given the full support of development tools and APIs specifically for their use. Minecraft would be a platform for a myriad of amazing games. Now people are doing that anyway, but the progress is significantly slower and Mojang actively impedes this progress through implementing more features that only a fraction of the community care about.
Minecraft passed up on the long-term business decision of becoming a platform upon which hundreds of good and fun games rely and instead opted for the short-term route of continuing Minecraft development conventionally and deallocating resources from it to work on other projects. The damage this does to Minecraft's future is palpable and frustrates me every time I play.