omg its so simple
the droids were universally acknowledged as the enemy, as the seperatist army. palpatine wanted to maintain the illusion that the clone wars were necessary and not something he just created to make everyone in the galaxy dance like puppets, so he got rid of them. wouldnt do very well to have the entire population witness clones and stormtroopers marching together and come to the realisation of what actually took place, would it?