I'll try and answer your question in reverse order:
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A question, in HOI do the Germans have a prediliction (i.e. national advantage) for tanks and the British for navy, or is it a choice the players make based on the strategic position in which they find themselves, which would be reversed if you moved the British player to Germany and the German to Britain? (I had the impression you were saying it was the latter, if the former then I'm less impressed with the design. I think we should aim for a system which produces the second effect if possible.)
It is some of each, but really the latter. The only way in which it is a 'national advantage' is that they start with more of that technology. One thing I am wrestling with is the controversial notion of not focusing exclusively or even mostly on the classic Orion setup of 'everyone starts with one planet.' This has produced, in all three MOO games, a situation where there is really very little diversity in playing styles. You cannot play as a pacifist; you must conquer, and you must build the most number of the largest ships (except in MOO1, I seem to recall, where having hordes of smaller ones was useful). There is never an advantage to building a corvette instead of a battleship. And while I'm leery of making decisions based on a combat system we haven't designed yet, I know that one of the cornerstones of what I intend to propose is that we -must- somehow emulate aspects of combat engines like Total War or Homeworld (more the former) that give actual, strategic advantages to each unit; light cavalry (the corvette in this case) is useful because of its speed, its ability to pursue routing units, and it is sometimes used as a long-range missile unit rather than for cavalry charges. This is the kind of distinction I think we need to really make a great game. I cannot admit to having the whole thing designed or even say that FO will choose to go that route, since I am only one voice of many; but it is a defensible argument, anyway.

Back to your question: It's really based on strategy. The British player could choose to forego their navy entirely; they risk losing their many convoys from their colonies that bring in necessary raw materials, but the gamble is that they could reinforce Belgium and the Maginot line enough to keep the Germans from ever getting to the point where Vichy France was created. There are several ways to play as all of the nations; in one game as the US, I spent a lot of time influencing Italy away from Germany, so they never joined the Axis. That is also quite a gamble, but it happened to work for me in that occasion; it quite easily might not have.
If you reversed the British and German players, their strategies would change quite a lot, yes.
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If we design a research system based on one from a game with these distinctions, because we like the way it works out in practice (which I think I'm beginning to see), but the system we're basing on works because of the distinctions, and we don't have those distinctions, will the system still work? What do we need in order for it to work? I think those are the kind of questions that need to be thought out, partly because they're relevant for the design of the research model, but also because they feed into the general design concept.
This is really the heart of this entire discussion. It is difficult for a project like this to plan out the part of the game we're in without also designing something that isn't slated until later on, but we really cannot do it in total isolation. I am arguing as though a model for space combat looks somewhat like what I'm planning will turn out; it may not, and it may be that we will come back and revisit the tech tree in 0.4 and 0.5 and change the whole structure. I think the tech tree has to be mutable all the way through the game, that we have to evaluate it at every step. But this is also dangerous, because the people we have here and contributing now are very different from the people we had when we were designing v0.1; and part of my job is to maintain some consistency, if, for example, everyone buys into some of what we've been discussing now and then the crew hates it for v0.4.
The core of my argument so far:
- A working research tree can be defined as one without (m)any easy exploits, in which the same player would follow different paths through it depending on their strategic situation;
- None of the MOO series ever had a working research tree, as defined;
- While we must be careful of designing anything in this early phase based on assumptions of what will happen when we're building the space combat engine, we must also guard against making assumptions based on how MOO chose to solve these problems; I consider it more likely that we will develop a system that has more in common with games that influence us now than we would reproduce most of features of any of the MOO combat engines; that is to say, I do not give additional credit to a solution to a problem simply because that is what MOO did.
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On the other hand, the second part of the paragraph is heading dangerously into "There will be no problems in this game's design because we'll balance it so well...". Which is pretty much the line the Moo3 developers took when people said their design was overcomplex and unlikely to work. (This sounds rather unpleasent, it's not supposed to, but my drafting skills are not up to improving the tone today.)
That's actually the opposite of what I meant. MOO3's solution to avoiding problems in the game's design was to hide most of the design from the player, and to change random pieces of it every time you played. Also, though, MOO3's 'design' changed 6 months before it was released. I have spoken fairly extensively with Alan Emrich about their process in the interests of dispelling rumors and seeing precisely what lessons could be learned, and it is from him that we got our mantra of #1) KISS (no rule that could not be calculated or explained by a human player) and #2) Steal what works before building a new system; there are very few 'new' systems and the real danger of pride is thinking that we can, from scratch, do better in terms of raw, fun-game design than people who have been doing this for decades and not borrowing what works on those grounds. Perhaps we can do better on some things, but I subscribe to those two rules.

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Fundamentally, the idea of a broad, balanced tech tree with multiple viable routes is only going to work if there are really multiple viable playstyles, other wise everyone will have to take the same route, because they are all essentially persuing the same strategy.
This paragraph contains our goal and our challenge. The idea of a broad, balanced tree with multiple routes only works with multiple playstyles; therefore, we must labor to support multiple playstyles in everything we do, and this is a prime example.
my brain hurts now.

good discussion!