The most annoying thing in Java without an IDE (and a source-control plugin for that IDE) is moving types from one package to another and renaming types. Due to the requirement that the directory hierarchy mirrors the package structure and that every public class is contained in a file with the same name this can be a bit annoying at times. Otherwise C# is much more concise for many things but apart from that there isn't much difference, at least for me.

To my knowledge C#/.NET has far superior language tooling included in the box with Roslyn. They also mention some sort of Omnisharp support.

I have worked on C# with vim and mono, and I can tell you that it is a lot easier than Java on the command line (which I have done too)