If you're not going to be using it on Windows at all, then yeah, I guess developing directly on Linux would be better. Linux Mint isn't designed for programming, so it might not have all the development tools you want installed at first, but it should work fine. For C# you'll need to use Mono, and MonoDevelop.
Let me introduce you to a new concept:
IDE != Programming
I think you are over-complicating things here.
The only things you really need are a text editor and a compiler/interpreter, that's it!
And as you said earlier:
It might just be because it's what I'm used to using, but I never found it as easy to get things going in Linux. Too many things to manually configure, too many things to go wrong.
This is probably because you are too focused on using an IDE for everything.
What I meant by "If you're not going to be using it on Windows at all, then yeah, I guess developing directly on Linux would be better." was that, if the application will not need to be used on Windows, just Linux, then he may as well program it in Linux to begin with, to save having to then port it over later. Obviously not really an issue with Java, since that works basically the same in every environment, but pretty much any other language it is a concern. It's easier to build it for your target platform in the first place than it is to code it for something else, then find half of it doesn't work when compiled for Linux and you have to spend ages changing it all.
The rest of that paragraph was a seperate point. Linux Mint isn't designed for programming, so it has fewer development tools. That has nothing to do with IDEs at all - the last time I used Mint, for example, it didn't have any version of the JDK installed, which means you couldn't do any Java development even in just a text editor. And it doesn't come with any of the Mono development tools either, which are needed to compile C# - regardless of any IDEs, if you don't even have a compiler, you can't do much. None of that is particularly hard to install of course, you just use Synaptic and it only takes a few minutes. I was just mentioning it.
On the IDE point, while a good IDE is definitely not a requirement to be able to program, it's certainly really,
really helpful. Easy code management, snippets, templates etc come in handy, as do tools for easily integrating libraries into a project. But mostly, inline debugging! It is so, so, so much easier to debug code when you can step through it line by line, inspect variables at every stage of the process, and easily track down the exact location of any problems. Having to type stuff in a text editor, then manually call the compiler, with the only debug output being the name of the exception, the line number, and a call stack (and any debug output you manually add to your program).
When I was programming in Linux, I was using Java, before I switched to Windows (and Netbeans). I was basically just using gedit and javac to develop with, and it worked. Then I installed something totally unrelated (I can't remember exactly what), and it somehow broke my JDK install, which meant I couldn't get anything to compile. Even uninstalling Java, the JDK, and everything related then reinstalling them all again didn't fix it, I spent hours trying to work it out. Hours that would have been better spent getting some actual work done.