No one invests in markets that aren't already there. Microsoft would have to pay handsomely for for developers to start developing for their platform. $1000 was their best offer. And Microsoft charges $99 per year for a developer account. Android charges $25, one time fee. Apple charges $99 per year. Does Microsoft have a larger user base than the others? No, so why charge the same as the others.
Secondly, the Microsoft API list is pretty short. If you know anything about programming, these are essential to building a working app. They also don't pay on in-app purchases until every $200 dollars and collects a 30% fee off your app sales (same as Google). If they want to be competitive, they need to start lower to bring in developers.
Lastly, its not Supercell's problem to bring in new customers for Microsoft. They waited until September of 2013 to release an app for Android and users exceeded iPhone users even before then.
If a customer wants Clash of Clans, they buy a different device other than Windows Phone. Supercell knows this and wont change until Microsoft becomes a close #3

