Mono certainly aims for better integration into the Linux userspace, at the cost of portability. The emphasis of Java on portability / platform agnosticity is

Mono certainly aims for better integration into the Linux userspace, at the cost of portability. The emphasis of Java on portability / platform agnosticity is one of it's strengths and one of its weaknesses. It's part of the platform's identity. Comparing the two platforms about linux desktop development is almost nonsensical, since for mono, linux desktop apps is the selling point (GTK# is designed as the main GUI framework for mono, and it gives a native feel on linux), whereas Java has a much broader audience at the moment.