Small restaurant SW of CTM bus station: Try local restaurants and couscous
But if you really look for some great genuine Moroccan food (fresh and cheap local specialites), step out from the tourist streets and look for the first place where normal Agadirians stay and eat: this is the place where the people who know go. The restaurant was small with poor furnitures and very poor choice of food (chicken, fish and couscous, seasonal salad) but clean and the waiter/owner was very nice.

There are more expensive but still cheap restaurants for budget visitors around the square opposite to my hotel where I ate as well. Warning: beer, wine or any other alcoholic drinks are not available in cheap local restaurants.

Fish couscous or royal (with meat) couscous + local salad tasted great. You can watch how do they prepare your couscous in special pots - more in local custom tip. I paid below $5 per person (with a drink).