Does using a number of stacked EI or EE cores in the place of a bigger
one (respecting the know magnetic characteristics) would pose any
substantial difference?
Stacking two cores (for instance) so that the cross sectional effective area of the core doubles doesn't give you any benefit magnetically (see edit section below) over the single core so I'm wondering the reason behind the question. If you double the area, the magnetic reluctance halves, allowing twice as much flux to be produced but, it's spread over the same area therefore, flux density remains the same.
As an example: if a single core was on the verge of saturation, with two cores in parallel and the same current flowing and same number of turns, the double-core will be at the same point of saturation. Nothing gained.
If, on the other hand you replaced an I (from an EI core set) with another "E" part, the length of the magnetic field through the core will increase and this increases magnetic reluctance and therefore decreases flux meaning, the core won't saturate as much for the same ampere-turns.
The answer is - it depends how you stack them.
EDIT
The question is about transformers and a lot of applications of transformers have DC running in the windings. If DC is the dominant cause of saturation then there would be no benefit in paralleling cores to obtain better saturation figures except when you can reduce the number of turns because the AC inductance/impedance will have automatically increased when the core area increased. If on the other hand, the transformer is voltage driven and the dominant cause of saturation is the AC current, doubling the area also doubles the inductance: -
\$A_L = \dfrac{\mu_0 \mu_e}{core factor}\$
Where core factor is length of magnetic field divided by core area, hence inductance doubles if area doubles. If inductance doubles and the transformer is voltage driven then current reduces and flux density also reduces and this can prevent saturation when it is the AC that causes saturation problems.