LLVM is a great tool, but I've had trouble in the past with version compatibility. I wrote a compiler that used LLVM as a backend (I used LLVM versions 3.4-3.6). The problem was that each minor version of LLVM slightly changed the API. It was things like removing parameters from methods, renaming methods, removing the need for some methods completely, or adding/removing some static-link libraries. If you only wish your tool to be compatible with a single version of LLVM, its not a problem, but attempting to support a selection of minor versions ended up being a pain. These minor versions would come out 3-4 times a year and I would need to find what broke each time, and if there was even an equivalent solution in the new version.

I didn't work on the level of IR, so I didn't come across any problems there, but I wouldn't be surprised if the IR syntax changed slightly across minor versions.