When you get the sand you can't see the gold nuggets so you just have to sit and wait for you income to go up, makes this stage of the game kind of boring.
Your upgrading system IS NOT UNIQUE! There is popular game for the super nintendo called Gradius with the same upgrading system. This game is almost 100% exatly like it, only for comp.
A good way to fix the wall problem is let the walls have health and the penguins can attack it. Seems like a quick fix, rather then going back and playing around with the A.I.
Never had a super nintendo and never played that game, but I hear a lot of people saying the same, I better check it out.