Bubble size and deformation are important factors for the closure models required in Euler-Euler simulations of bubbly flows. To properly simulate polydisperse bubbly flows where the bubble size spectrum may cover a range of several millimeters, several velocity groups with different sizes have to be considered. To this end, the theory for the particle-center-averaged Euler-Euler model is generalized for the simulation with multiple bubble velocity groups. Furthermore, bubble deformation effects have been included in appropriate bubble force models. The particle-center-averaged Euler-Euler model provides additional freedom to consider the bubble shape during the conversion between the bubble number density and the gas volume fraction. Therefore, the theory is also generalized to consider an oblate ellipsoidal bubble shape in simulations. A bubbly pipe flow is used to validate the theory and to demonstrate the improvements of the proposed generalizations.