In particular, attempting to use it with npm modules is an exercise in tedium, as its module resolution constantly breaks and bizarre, undefined behavior does not stop happening. I've found dozens, maybe hundreds of similar reports online, with no solutions offered. There are all sorts of arbitrary gotchas with its configuration as pertains to this and other things. "Oh, don't use outDir and it'll work."
While it has great and straightforward integration with VS Code, it has disastrous integration with Visual Studio 2015 and 2017, the latter of which does not even support updating the bundled TS version at will without registry hacks. While TS emits code even in the case of errors, in many situations, Visual Studio refuses to complete the build process in case of TypeScript errors.
For an ES6+->ES5 transpiler, it is also very strange in that it polyfills some things but not others, such as Promises and Maps.
TypeScript has ultimately brought an unacceptable overhead to my project. It does not get out of the way as soon as you attempt to use it with the rest of the ecosystem. There belies its arrogance: it treats JavaScript as a second class citizen and favors Typings (additional files that assign types to plain JavaScript libraries). But in most cases, Typings are outdated, or nonexistent. Only recently has support for plain JavaScript libraries gotten better, with the AllowJS and CheckJS flags, the latter of which Visual Studio 2017 does not recognize for whatever reason.
In my view, it comes with so much baggage that it's probably not worth using. Some of the solutions proposed by the project maintainers amount to writing boilerplate just to support JavaScript functions. It's essentially C header files: you have to write module declarations for certain plain JavaScript libraries to work. There are different versions of this boilerplate that you could be asked to write: you may be told to write a typings file (i.e. declare every single function of the library you want to use in a separate file, and add it to the project, possibly using ///<reference> in certain specific scenarios). There are also ad-hoc declarations of modules and constants/globals that you may or may not need to write (there is no idiom here, and the language regards this as going off-road).