Well, the obvious one is your deployment options: You need to either compile binaries for the target platform, or ask the user to compile from source. As far as I know, you can't yet compile Rust to Javascript.

Support for GUI toolkits will probably require some glue code. I've heard that Windows is a particular source of headaches, but I'm not clear as to why. SDL seems to work everywhere; remember that Rust is designed for seamless C interop in both directions.