I read that fruit sugar isn't stored as muscle glycogen...
Wrong, fruit sugar can and will eventually be turned to glycogen.
Originally Posted by Simplicio
so If I were go to the extreme and replace all my complex carbs with fruits like apples, pears, bananas, will I still gain muscle?
Why would you do this? Eat all complex carbs: leafy greens, veggies of all sorts, fruits, and whole grains. To answer your question: Yes, I suppose your sole source of complex carbs could be fruit and you could still build muscle assuming all other macronutrient consumption was appropriate.