The current way of balancing food items is to make single items (apples, crops etc) restore next to no hunger. This is supposed to encourage players to craft more complex meals to refill their hunger bar, but there are other ways around needing to make vanilla foods useless;

Instead of simply altering the amount of hunger basic foods provide, the more advanced meals could provide additional long-lasting buffs, similar to how you eat golden apples in the vanilla game to gain additional hearts and regeneration.
Different meals would provide different buffs, though these wouldn't have to stack to avoid being overpowered (optional perhaps). This would both encourage and reward players for making the larger more complex meals, while keeping lower tier foods survivable.

Newer versions appear to take a more elegant approach (labelling food as fulfilling or hearty), going to consider this solved.