The fact that I can add TypeScript to any project's workflow by simply `npm install --save-dev typescript typings` is a massive advantage. The tooling around typescript is much better as well (typings + definitely typed for example). With TypeScript 2.0, I'm not sure I'll have any reason to use Flow anymore...
The differences are in tooling.
I have tried to use it ~6 months ago and the tooling felt kind-of wonky and I didn't feel like maintaining the interface files if so much of it seemed to be in flux.
In terms of type definitions available for third party libraries, Typescript is way ahead. I also think the documentation and community around Typescript is stronger, and will only get more so with the move to use TS as the default in Angular 2. Also the stability is great and the roadmap looks promising.
Nothing against Flow, I think it is great and definitely has some advantages (and anything which adds types to JS is a winner in my book!), but it feels slightly more like an internal Facebook tool that happens to be released to the public versus Typescript, which is more of a release quality product.
But yeah, either is great improvement over plain JS and I'd definitely consider Flow for a personal project, but in a bigger company/team environment I think the stability, tooling and community of Typescript would make me push for that.
Refining the .flowconfig so it worked universally also took a bit of time, but that's more due to our very large codebase than flow.