Here's the reason in a nutshell
Quote:
There’s a certain inherent incompatibility between what we want to do and what they want to do.
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It's odd, but with EA, I had the impression that EA is only doing this for monetary reasons. With Notch and Minecraft, it literally seems that he cares about how he's affecting the user base, splitting it up unnecessarily. Sure, you can add the game to your Steam games, but integrating it into the API naturally is an entirely different story.
While there's no big rift between Notch and Valve on this, it is rather telling that for all of the advantages Notch may have on Steam, he chooses to keep close to his customers with the system that works best for him and his company.