We use large-scale simulations to study the microstructure and concentration fluctuations in sedimenting suspensions of anisotropic particles such as spheroids, and deformable particles such as viscous droplets in the Stokes flow regime. An efficient method based on point-particle interactions is used allowing the simulation of full-scale suspensions with both periodic and slip boundary conditions, where the latter are used to qualitatively reproduce the effects of container walls. The concentration instability occurring in such systems is adequately captured, and we show that the formation of inhomogeneities is closely linked to the large-scale fluctuations of the disturbance flow. In particular, our simulations suggest that the presence of walls is important for a wavenumber selection to be observed, as they lead to a decay of the initial large-scale recirculation that otherwise dominates the flow in periodic systems. Results for the sedimentation rates and orientation distributions are also presented, and show good agreement with published experimental results.