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I'm not planning to write anything that really needs the extra speed C++ provides

C++, as a language, provides no "extra speed" in general. Languages lack performance; performance is only relevant in specific scenarios. Do not fall into the trap of believing that C++ will perforce make all your projects faster. Furthermore, you will be the limiting factor in terms of performance of your projects for some time to come, not the language.

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so first I thought I'd use Java. I pretty much finished a basic arcade engine I can use to write simple games, but the more I write the more I dislike the restrictions of Java..

What restrictions are those?

In general you're going to be most productive with the language you know best, which seems to be Java at the moment.

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But I'm wondering if I should go with C# instead, what would you suggest, which language is better suited for game development?

I like C#. I would recommend it -- also Python -- in the general case. However, it's entirely possible that you'll discover you have the same dislikes of C# (or Python) that you do of Java. So you should supply an answer to my prior question concerning what you dislike about Java, and I or somebody else will be able to advise you further.

What OS functions are there you must have? I'm certainly not a Java man but it allows you to read/write files, do directory operations, use sockets, use OpenGL. ie pretty much anything and everything you would really need to do.

C# isn't going to get you any closer to the OS then Java does. To a programmer the CLR isn't really much different then JVM.

If you are worried about being close to the OS then you should stick to assembly or whatever else it was you used before.

As far as good support for threading and networking, it doesn't get much easier than Java and C#. In both of these languages, the support is built into the core language libraries themselves, so you can do tasks in fewer lines with less fuss than what it would take in other languages. You definitely won't be messing with "basic networking". It is all pretty streamlined.

If you want to make extensive use of networking and threads, I think you may need to weigh how important these OS functions are to your game development. Besides those mentioned by the poster above (file access, etc.), which are all built in to Java and .NET, I am not sure what else game development needs. The added benefits of VM threading and networking may be more than worth the loss of these OS functions which are rarely used in game development.

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C++ is compiled and therefore execute alot faster than a language like python

Being "compiled" has about as much to do with its performance, in the general case, as being written by a fellow with a funny name. In general, making relative assertions like this is just masturbation. What matters is what you're actually doing. Furthermore, this is not the forum to be making these sorts of declarations in, as it is frequented by impressionable neophytes. If you want to instigate a discussion about performance, take it to General Programming or some such. I expect there to be no further discussion of the matter in this thread.

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I've got about ten years of experience with programming, most of it in malware and security programming. Something I'm no longer proud of, but I've got pretty good experience with very demanding programs and applications.

Okay, then you should be capable of making any suitable (non-toy) language run efficiently enough to make a good game.

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I want a language that will let me work with the OS pretty much unrestricted.

C# will let you use platform-invoke to access OS capabilities that are not directly exposed by the BCL, although you will of course be sacrificing cross-platform capability in doing so. However, mono doesn't have the greatest support for the non-core aspects of .NET anyway (such as Windows Forms), so maybe this won't be a big deal.

So it sounds like C# will work for you if you really want to abandon Java. I'd still vote for sticking with what you know best, but the transition to C# will likely be painless (if you don't know it already).