Any ideas on how to accomplish some of this?
It depends on whether or not historical credibility matters to you. If it doesn’t matter to you at all, then the answer is very simple: you simply operate each player nation as a separate entity which is free to ally itself with whomever it wants and to make war against whomever it wants. I think this concept was once described by somebody as a “free-for-all” game. It gives you maximum flexibility (something which your group seems to be interested in), at the expense of having little or no “narrative” driving the game (meaning that there’s little or no background story – at least no credible one – explaining why the nations of the world are behaving this way). I don’t have any personal interest in this approach, so I’m not in a good position to describe its advantages, merits, or operational details.
If, however, it does matter to you for your game to have some sort of plausible background scenario, here are a few ideas. I’ll limit them to the WWII era, since that’s the historical period in which I have the most interest.
One thing you could do is to make the complications of WWII work to your advantage. As Richard Overy explains concisely in the opening note to his book Why The Allies Won, the terms “Axis” and “Allies” are actually imperfect labels for two broad coalitions whose composition changed at many points during the war, and many of whose members were, at various times, not even actually at war. This resulted in all kinds of situations that look odd, when you view them from the perspective of the US, the UK, the USSR, France, ANZAC and China being on the Allied side and Germany, Japan and Italy being on the Axis side. Just as three examples: France and Britain considered war against the USSR in support of Finland in 1939; the British attacked the French fleet in 1940; and Germany attacked the Italian fleet in 1943. So you could play on elements like that to generate some alternate game scenarios. What if, for example, Germany and the USSR had remained allies under the Molotov-Ribbentrop Pact? (A scenario like that is discussed in the book “What If?: Military Historians Imagine What Might Have Been”, under the title – if I remember correctly- of “Triumph of the Dictators”). In other words, play around with different alliances between the major powers, while trying to keep then plausible. Then, once you’ve set up these alternate power blocks with the main nations, throw in some more variation by taking the various neutrals/minor powers and attaching them to these new power blocks, in ways that were perhaps different than was the case historically.