Mainly because I was already using babel (which was 6to5 at the time). Typescript didn't support JSX at that time either. I don't know if TypeScript has full ES6 support yet? (And async/await!)

Overall babel seems to be moving in a direction which I'd consider really interesting. With babel 6 you'll be able to write a plugin to add runtime checks that aren't limited to module boundaries.

Not the OP, but I use flow because (1) it's easy to integrate into an existing project without having to define and rewrite everything with types and (2) I've found myself using other Facebook tools anyway (mostly in the React ecosystem) and Flow tends to be better supported in that world. But I hear the IDE support for TypeScript is first-class, something I haven't found to be the case with Flow, which interests me.

One particularly relevant feature of Flow is that it does its type checking in a server. It watches the file system and incrementally rechecks automatically when files change. With this setup, "running" the type checker is actually just querying the server, which returns very quickly.