I want to grow a small garden with few plants as possible with efficiency in nutritional value in mind. What plant in the world has the most nutrition from the roots or the flower?
Sweet potatoes. They are so nutritious that it makes up between 70 to 90 percent of the total calorie intake of longest living populations around the world like Okinawa Japanese, Papua New Guinea Seaside islanders, and Papua New Guinea Highlanders. And it's one of the official foods that NASA provides for its astronauts.
There are many different important qualities found in foods, and no food provides all of them. So it's impossible to say that there is any single "best" food, and that's why it is essential to eat a variety of foods. If you wanted to know which plants are best at providing a specific nutrient, that would be an answerable question.
Similarly, there is no single plant that is best for a garden. Not only is it important to consider your circumstances (season, latitude, rainfall) but also many plants grow best when planted in combination. For example, this question on Gardening & Landscaping explains why corn, squash, and beans work well together.
You have one contributing to the structure of the growing environment above the soil, one affecting the richness and suitability for growth within the soil, and one protecting the surface of the soil.
It sounds like you're looking for plant recommendations, so you might have better luck asking on the Gardening site and using the tag
This is an impossible question to answer, as no plant contains everything that you need.
Here's a few remarkable ones though.
Sweet Potato - High on a very large spectrum of nutriments.
Avocado - One of the best plant-based sources of fats.
Spinach - Extremely high in iron, folate, and vitamin K.
Kale - Similar yet alternate stats to spinach, most remarkably higher in vitamin A, C, and K
Almonds - Very high in a ton of minerals, vitamin E, riboflavin, a plethora of fats, protein, dietary fiber.
Walnuts - Slightly lower than Almonds in most things (which is still great), but boasts the highest non-processed amounts of poly-unsaturated fats in the world.