We define a novel quantitative strategy inspired by the ecological notion of nestedness to single out the scale at which innovation complexity emerges from the aggregation of specialized building blocks. Our analysis not only suggests that the innovation space can be interpreted as a natural system in which advantageous capabilities are selected by evolutionary pressure, but also that the emerging structure of capabilities is not independent of the scale of observation at which they are observed. Expanding on this insight allows us to understand whether the capabilities characterizing the innovation space at a given scale are compatible with a complex evolutionary dynamics or, rather, a set of essentially independent activities allowing to reduce the system at that scale to a set of disjoint non interacting sub-systems. This yields a measure of the innovation complexity of the system, i.e. of the degree of interdependence between the sets of capabilities underlying the system's building blocks.