Why do you suspect this would be problematic?
We'll get to that in a minute...
I'm reading Fantasy Craft and am finding that it treats powers, abilities, rewards, and story elements as different sorts of resources with their own similarly conceived systems of adjudication. Yet there is still an important place for the GM.
I'm not familiar with that product. However, I note that you report they are all
different sorts of resources, each with
their own systems for adjudication. That's fine. It seemed to me we were talking about making them all, in essence, the same resource, and that I find problematic. They are apples and oranges, and ought to be managed separately, IMHO.
I now return to the original premise once again - that levels are the base for the adventure design. In general, for RPGs, this is patently not true. While D&D and the various D20 variants have them, most systems
don't have levels. All the White Wolf WoD games? Point buy. GURPS? Point buy. Shadowrun? Point buy (and money-buy). The list goes on. Levels are fairly unique to D&D and its direct descendants.
Ergo - in general, for RPGs, levels are not that integral to adventure design at all.
Have you guys ever played a point-buy game, by chance? If you think that levels are so integral to games, then perhaps not. They have their own strengths and weaknesses - in fact, the basic strength of point-buy is also it's basic weakness.
Point buy systems are, by their nature, far more flexible than systems that use levels - players can buy all sorts of different abilities, and tailor their character to be exactly what they want (or as close to as the rules will allow, anyway). However, that means that a character can often be built haphazardly, so to be minimally effective, or in so focused a manner as to be nearly broken*.
The same flexibility that allows players to get what they want makes it more difficult for the GM to deal with that situational change in power. Challenging the combat-optimized characters without killing off the non-optimized characters is harder in a point-buy system than in D&D. In D&D, the GM can at least count on certain minimums of hit points, saves, and so on for characters of a given level. The same cannot be said for point-buy.
Now, take that one step further. All the "advancement" is pooled together. I now have to try to balance an adventure for the guy who has focused on getting combat tricks with the guy who has focused on getting the narrative-based bennies (say, favors from people of note). That becomes... downright ugly.
If they are separate resources, I can manage them separately - make sure the characters are more on par in each field separately. That isn't as easy if they are all unified as "development".
*People who think that some 3e feat combinations and class powers together are broken ain't seen nothin', until they've looked at some of the ugliness that you can do with, say, GURPS Supers. Yeek!