At some point, I think we'll be limited by limitations in the way we think, rather than the inputs (media). Humans think by spatializing[1] (I'm using Julian Jaynes' definition here). Which is why pen-and-paper and electronic analogs thereof endure -- it's a 2D version of what goes on in our mind.
Moreover, things that in the physical-behavioral world
do not have a spatial quality are made to have such in
consciousness. Otherwise we cannot be conscious of them.
This we shall call spatialization.
Time is an obvious example. If I ask you to think of the
last hundred years, you may have a tendency to excerpt
the matter in such a way that the succession of years is
spread out, probably from left to right. But of course
there is no left or right in time. There is only before
and after, and these do not have any spatial properties
whatever — except by analog. You cannot, absolutely
cannot think of time except by spatializing it.
The goal of Bret Victor's interactive visualization work is to take concepts that are inconceivable (because, as you say, they are not immediately tractable to spatialization) and, through clever transformation, MAKE them conceivable. Are there "inputs" where this doesn't work? Maybe — but I'm not sure where they could be found in nature.
Does everyone think spatially? There are those who lack a "mind's eye" entirely, which seems like it would at least help with spatialization, and I've worked with businesspeople who said they thought entirely in terms of time, and space was a much less concrete concept for them.
[1] http://www.julianjaynes.org/origin-of-consciousness_english_...