In essence, you want to destroy the slippery slope while allowing fatal blows if the enemy is careless and have a strong focus on economics.

Yes. I think essentially, I'm replacing the "tech upgrades" of many 4x games with "economics". Taking the right planet allows you to get back in a game you would otherwise have lost. The upside is that, unlike a game where fixed research points are earned and you keep growing stronger, even if you lose a few planets, here, you constantly need to focus on your most prized planets, else you'll lose your advantage (whereas you don't lose techs for example).

How about associating rare resources to a given counter? You retain the base resources used in every ship. For advanced components, you add a rare resource. Its counter component would require another rare resource.

I like to think that all resources are rare: after all, they are finite in numbers, and even if they appear abundant, this will be the case only for a few more turns than an actually rare resource.
Your suggestion, if I rephrase correctly, is to use a certain number of "regular resources" which are generally common and can be found on most planets. They are essential to building stuff such as ships. Everyone needs them, and you can exist using them alone.
Then, you have another layer of resources which are considered rare, or hard to acquire, and are tied to specific counters. For example, you can build ships and beam weapons with regular minerals, but to have extra armored hulls and armor piercing beams, you need a rare resource (say, duranium for extra armor, and titanium for armor piercing, or whatever).

Also, you would be unable to mine everything. Even if you have lots of planets, fuel costs would prevent you from ferrying it all. Choosing which resource to mine, ferry and refine becomes part of your overall military strategy. That will reduce the slippery slope effect.

My initial intent was to allow players to mine dry fuel-planets (gas giants or the likes) and use that excess fuel to bring freighters to planets that have been mined dry and ferry all of the minerals back. This is why I'm working with the assumption that resources are finite and rare, in general.
I'm not opposed to the new choice you're bringing to the table though. Having less fuel in play will demand that the players choose what they ferry: instead of mining dry every planet they can and, automatically, bring as much back as is necessary, having richer planets with less fuel to be mined will force them to think ahead and bring only what they really need.

You might find common materials on half the planets

That's harsh But why not... Assuming there is room for industry-planets, that might as well work.

and rare ones on 5~10%

That's a bit under the Molybdenum rate, but this makes sense. Numbers need a bit of fine tuning, but I understand your idea better.

And I agree, fuel is the backbone of the economy. Everything can be measured down in value in terms of fuel it costs and earns (including warships).
This was one of the weakness of many players in VGA Planets: they kept building the largest warships, loaded them with fuel, and went away:
- Weight of the fuel itself caused fuel to be used at a higher rate because the ship was even heavier.
- A lot of what they packed in (230 torpedoes, really?) was not necessarily useful immediately, which added even more weight.
- In case of a warship being destroyed, they lost the fuel.
- It was slowed down by its weight, which means it could cover less ground at a lower speed, thus further decreasing the area of influence gained from such a warship.

A good player would probably only build a few of these and position them (idle) at key places, ready for necessary responses, only against tough opponents. Everything else could be under the vigilant eyes of light cruisers and scout ships.

Such model would promote turtling (which might be good or bad, depends),

Not really, since you're always in shortage of fuel (because of say, domestic consumption alone) you're always on the lookout for new planets. You move scouts and find planets, then colonize them, and concentrate force to defend them but that's hardly turtling.
Also, you can balance shortage of other minerals so that its relatively easy to build a weak ship, but incentivize users to save up and build stronger warships.

Regarding WWII:
http://vanrcook.trip...uelshortage.htm

Interesting insight into WWI cause and effects and even Iraq as conflicts motivated by scarceness of fuel wouldn't you agree?

Yes, but it's always about the price of the fuel, not about the total lack of it.

Then again, space conquest is in the foreseeable future. Some serious experiments involve using water as fuel because of the scarcity of fuel left as we speak, so I don't think it is very sci-fi to consider shortage of fuel.

In a game you usually have no trade and "minerals alchemy", so it might lead to "I have these 100,000 tons of titanium, but hey, I have no fuel so lets dump it since it's totally useless".

VGA Planets had mineral alchemy at higher levels, which was the one feature I actually didn't like. Not everything can be turned into everything else just so that its convenient. I like the way fuel is finite and represents a threat of its own.

In a real world situation you could always sell the titanium to obtain all the fuel you need (to the point where the relative price of titanium and fuel will become balanced).

To the point where titanium would be worthless you mean. In a real world economy, if your supply is larger than demand, the price lowers and won't stabilize at the same price as another commodity. It will keep going down:
StarKnights emulated real world economy very well, to the point where selling abundant coal and petroleum to get rare crystals would eventually lead to an inability to sell your products altogether (whether because there was simply no demand throughout the galaxy, or just because the price was smaller than 1)

In a real world you would never have a shortage of fuel (long term at least, short term is possible), it just might be prohibitely expensive.

This is a Maltucean view, which has since been discarded by most scientists. He believed that lack of finite resources would translate into a means to find an alternative solution to the problem (much like Hybrid cars translating into electricity-fueled cars by lack of fuel). The truth is that it often applies, but not always.
One good example would be Voyager or Curiosity. They pack RTGs as their primary power sources, which has a half life of 87 years and packs 50W per cell. You'd be led to imagine that this is a very potent alternative to fuel, but you'd be wrong, and here is why:
- Cost of production for a Plutonium cell is considered to be a few millions at the moment, and because it is even rarer than fuel, don't expect a massive decline in costs.
- Radiation levels imply that this is ideal for an unmanned shuttle or vehicle, definitely not for a space-crew.

In other words, alternatives to common commodities exist, but they often are a very specific solution to one of the problems initially solved by the resource. Fuel is widespread in use and purpose, RTGs, not so much, electricity-powered cars couldn't launch a space shuttle into orbit and sustain a year-long space expedition.

But don't forget that "expensive fuel = defence is better than offence", if you go too far that way you could make it all about turtling.

Defense plays an important role. And offense is mostly a question of scouting/information.
I don't envision this game to be aggression-based. The reason why turtling will be impossible is that it requires concentration of force. But by design, the game will require you to spread out across different planets.
Thus, you can turtle on one or two planets, but doing so means you'll be extremely vulnerable at your resource colonies or production centers, which you can't afford.
I would speculate that some of the best strategies would include having a lot of weak forward outposts with fast scouts, just to get a visual on the enemy fleet, and then, moving your own to engage where you expect them to hit.
Alternatively, having a few warships on border planets would also make sense, so long as they're fast enough to make chase should the opponent's fleet pierce across the border lines and go deep in your cluster.
I just don't see a viable strategy that involves turtling all planets at once with enough strength to defend it all against outsiders, plus if you can, this means you'll have nothing else you can invest on, meaning that, in the long run, your economy will be crippled compared to your opponents which have chosen to expand aggressively.

One key decisions would be to decide when to expand, and take advantage of an opponent turtling by aggressively claiming more colonies and eventually overpowering them with even more ships, but that's an endgame I would find less satisfying and I would anticipate a clever player would understand that turtling altogether is not a viable strategy, but that going all out isn't either.

You could counter it by giving some advantages to attack (like ambush bonus, or something).

Picking off undefended freighters or lightly defended convoys would be just that: a quick way to capitalize on resources by, not only removing them from your enemy's zone of influence (and thus cripple their economy) but escort them back home to yours, and increase your economy. Any given efficient raid against enemy freighters results in a potential gain, without the need to strike at a planet or base.

Personally, I would make all ships use fuel all the time which would make fuel completelly transparent to defence/offence desirability (but that has obvious disadvanages in terms of the realism).

I see fuel as a cost of option, in relation to the speed at which you want things to happen. It is a means to define priorities. For example:
You want your warship to reach a planet:
- If time is critical, you might want it to reach that area for the next turn because of imminent conflict, thus forcing the fastest speed (and a very taxing fuel cost).
- If time is not critical, you might want to save up on fuel, accepting as much as a 3 turns delay, knowing that the fuel cost will be so low that the ship will still be able to easily make the trip back.
- If you intend to explore to the outer edges of space, you might actually accept a delay of 5-7 turns to that planet, knowing that the fuel cost will be so low that your ship will be able to go across the galaxy before meeting fuel shortage

Well, it all is about numbers. Depending how you set these values it might be a problem or no problem at all. Just don't go "it's all about fuel and about fuel only"

Fuel is vital, ut what's fuel without a ship? Most other components find their inherent value in the fact you need a fleet before you need fuel. They will all be indirectly related in ship building, even if only remotely (building mines requires minerals that may not be necessary in a specific ship design, but you still need to have the mines up first).