Flow's tooling was a nightmare last I tried to use it. It seems custom built for a very specific purpose -- incrementally adding types to an existing legacy codebase. Typescript's tooling works seamlessly with webpack/babel/etc.
Less important, but you also have to add /* @flow */ to the top of every single source file. Sure its handy sometimes for existing projects, but it makes little sense for new ones and has also been an issue for years[4].
[1]: https://github.com/facebook/react/blob/65b9ad94aaf62eb61b7b3... [2]: https://github.com/babel/babel/blob/634c750558e5ce149b879b66... [3]: https://github.com/facebook/flow/issues/869 [4]: https://github.com/facebook/flow/issues/284