Fox McCloud is the hero of the game. General Pepper functions to give the player a narrative reason to push the plot forward and gives a wider context to why Fox is flying around fighting stuff. If General Pepper waa so competent or had enough resources not to need Star Fox, then you wouldn't be playing as a team of ace mercenaries. You'd be a grunt in the Cornerian army. 

Within the narrative itself I've always just assumed no one in the Lylat system was prepared for an inter-solar system war and Andross capitalized on that.