I suppose the problem is that I see typescript as the fragmentation. If MS leverages babel (they can even keep shipping TS as their own thing if they want, I just want them to provide babel plugins), we can all use that and focus on making it as cross-compatible and streamlined as possible. (Well, really, we can focus on providing a single well-documented on-ramp to new javascript developers, which I think is the main problem and the one MS set out to own with typescript.)
Right now, we have the typescript ecosystem, the babel ecosystem, and the other wannabe ecosystems. If I like Typescript's type system but want to use babel for async-await (for instance, I'm aware it's in TS next), I'm basically SOL. Babel has more end-users (AFAIK), generally has the first/only implementation of <feature>, and my impression is that the surrounding development community is larger and more active (typescript stuff tends to come down from On High).
For instance, you can use https://github.com/gcanti/babel-plugin-tcomb to get run-time type checking with babel/flow for free. That's really cool! Unfortunately, the same is not possible with typescript (AFAIK), because MS decided that was out of scope. If Typescript was offered as a babel plugin, somebody else could implement it for typescript and we could all be happy.