Tim Schafer seemed fairly honest about the decision to sell Double Fine Productions to Microsoft at E3 - it all came down to the money. While he (may) have been joking, he has given some fairly compelling reasons why he feels the move was the right one, and speaking to Gamasutra, he further explained the decision behind it.
To be fair to Microsoft, apart from enforcing Xbox & Windows 10 exclusives upon the studios they're soaking up, they've been more than happy to leave them as autonomous units that maintain their unique identities. Schafer confirmed as much, stating that Microsoft was committed to a "a new way of acquiring companies" and that the company would indeed maintain it's identity and spirit.
He believes that Microsoft will allow Double Fine to remain "experimental" without having to worry about getting their next publishing deal, or stressing over weather the bills were getting paid that month.
The great thing about the acquisition is it lets us refocus—it lets us focus at all—instead of making a game while worrying about all these other aspects.
It seems that Xbox Game Pass was another key deciding factor behind their decision, though. Schafer said he can see why having a company like Double Fine, along with other diverse publishers under the Redmond umbrella, will ultimately make the service far more valuable when their identities remain unique.