You too much romantize vanilla. Factions in it werent designed to be convient during progression on years scale. It was designed to be convient during your singleplayer campaign. Here already passed 26 years since vanilla events. From IRL history we know that not every movement, regime, state, exist even so long. So i dont see real problems in fact that factions changes, dying, merging, etc.
But i agree with you that when those changes were done, they werent done about right.
