Babylon merged TypeScript support yesterday [1]. This means that in the future it should be easier to setup Babel with TypeScript.
I agree with the decision to go with TypeScript. It has drastically better community support. Most third-party components won't have flow annotations. Flow would've been a lot more successful from the start if it had started out with DefinitelyTyped support. Heck, even now I'm still wondering why they don't do that.
[0] https://codemix.github.io/flow-runtime/#/
[1] https://github.com/babel/babylon/pull/523#issuecomment-31172...