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).
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.
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.
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.
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).
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.
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.
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.