Why do we choose apparent power rating as base in per unit analysis of a power system?
The capacity of the generation, transmission and distribution components is determined primarily by the apparent power. Also apparent power is always more than real power. Those factors make it generally more convenient to choose apparent power as the per-unit base. The key is convenience. There is no reason that some other base can not be selected if it is more convenient for a particular purpose. You can always work out some example problems using real power as the base and then again using apparent power and judge for yourself which is more convenient.