This is great! I once tried to do something like this but gave up because of all the potential complexities. It looks like you have many of them covered. This has a lot of potential if you expand it to "real world" living. A few suggestions:

  - ability to create and save custom templates of choices (beyond Atkins...)
  - "ALL" toggle for each food group
  - database of commercial groceries (Heinz baked beans)
  - database of restaurant menus (Big Mac)
  - templates of meal types beyond "breakfast" (post workout, TV snack)
  - fix breakfast option (seems to ignore when chosen)
  - seasonal menus for produce
  - a way to cook meals for multiple people with their own preferences
  - Natural Hygiene (Fit for Life, Fuhrman) template
  - consider pricing
  - micronutrients beyond carbs, protein, fats
  - consider allergies
  - raw options
  - notifications (email, text, msg)
  - historic reporting with suggestions (especially daily calories)
  

Best wishes for a great product. Please keep us posted.