C# Online Compiler | .NET Fiddle

<no name> by Anonymous

using System.Collections.Generic;
using System.Linq;
using System;
					
public class Program
{
	public static void Main()
	{
		var categories = SetupCategories();
		
		var cleanCategoryList = categories
			.Distinct()
			// I'm guessing you only want to compare subcategories if the top-category
			// Names are the same. So... group them:
			.GroupBy(c => c.Name)
			.SelectMany(group =>
			{
				var candidates = group
					// Create tuple containing the category itself as well as a set of
					// the names of the sub categories
					.Select(c =>
					(
						c,
						c.SubCategories
							.Select(sc => sc.Name)
							.ToHashSet()
					))
					.OrderByDescending(c => c.Item2.Count);

				var catsWithUniqSubCats = new List<(Category, HashSet<string>)>();
				foreach (var tuple in candidates)
				{
					// Since we sort by descending Count of the set of sub cat. names
					// we only need to compare each tuple with those already picked for
					// the resulting list
					if (!catsWithUniqSubCats.Any(c => tuple.Item2.IsSubsetOf(c.Item2)))
						// The tuple's category's sub categories are not a subset of
						// any other list of sub categories, so we add it to the result
						catsWithUniqSubCats.Add(tuple);
				}
				return catsWithUniqSubCats.Select(tup => tup.Item1);
			});
		
		Console.WriteLine(string.Join("\n", cleanCategoryList));
	}
	
				
	private static List<Category> SetupCategories()
	{
		var duplicateCategory = new Category
        {
            Name = "E-platform",
            SubCategories = new List<SubCategory> {
                    new SubCategory
                    {
                        Name = "App",
                        order = 1
                    },
                    new SubCategory
                    {
                        Name = "Layout",
                        order = 2
                    },
                    new SubCategory
                    {
                        Name = "Sidepanel",
                        order = 3
                    }
                }
        };

        var duplicateCategory2 = new Category
        {
            Name = "E-platform",
            SubCategories = new List<SubCategory> {
                    new SubCategory
                    {
                        Name = "Website",
                        order = 1
                    },
                    new SubCategory
                    {
                        Name = "Layout",
                        order = 2
                    }
                }
        };

        var categories = new List<Category>
        {
            //APP
            duplicateCategory,
            duplicateCategory,
            new Category
			{
				Name = "E-platform",
				SubCategories = new List<SubCategory> {
						new SubCategory
						{
							Name = "App",
							order = 1
						},
						new SubCategory
						{
							Name = "Layout",
							order = 2
						}
					}
			},
			//WEBSITE
			duplicateCategory2,
			duplicateCategory2,
			new Category
			{
				Name = "E-platform",
				SubCategories = new List<SubCategory> {
						new SubCategory
						{
							Name = "Website",
							order = 1
						},
						new SubCategory
						{
							Name = "Layout",
							order = 2
						},
						new SubCategory
						{
							Name = "Sidepanel",
							order = 3
						}
					}
			}
		};
		
		return categories;
	}
	
 	public class Category
	{
		public string Name { get; set; }
		public List<SubCategory> SubCategories { get; set; }
		public override string ToString()
		{
			return $"Name: {Name}, SubCategories: [\n    {string.Join("\n    ", SubCategories.Select(sc => $"({sc.ToString()})"))}\n]";
		}
	}

	public class SubCategory
	{
		public int order { get; set; }
		public string Name { get; set; }
		public override string ToString()
		{
			return $"Name: {Name}, order: {order}";
		}
	}
}

​x
 
using System.Collections.Generic;
using System.Linq;
using System;
                    
public class Program
{
    public static void Main()
    {
        var categories = SetupCategories();
        
        var cleanCategoryList = categories
            .Distinct()
            // I'm guessing you only want to compare subcategories if the top-category
            // Names are the same. So... group them:
            .GroupBy(c => c.Name)
            .SelectMany(group =>
            {
                var candidates = group
                    // Create tuple containing the category itself as well as a set of
                    // the names of the sub categories
                    .Select(c =>
                    (
                        c,
                        c.SubCategories
                            .Select(sc => sc.Name)
                            .ToHashSet()
                    ))
                    .OrderByDescending(c => c.Item2.Count);
​
                var catsWithUniqSubCats = new List<(Category, HashSet<string>)>();
                foreach (var tuple in candidates)
                {
                    // Since we sort by descending Count of the set of sub cat. names
                    // we only need to compare each tuple with those already picked for
                    // the resulting list
                    if (!catsWithUniqSubCats.Any(c => tuple.Item2.IsSubsetOf(c.Item2)))
                        // The tuple's category's sub categories are not a subset of
                        // any other list of sub categories, so we add it to the result
                        catsWithUniqSubCats.Add(tuple);
                }
                return catsWithUniqSubCats.Select(tup => tup.Item1);
            });
        
        Console.WriteLine(string.Join("\n", cleanCategoryList));
    }
    
                
    private static List<Category> SetupCategories()
    {
        var duplicateCategory = new Category
        {
            Name = "E-platform",
            SubCategories = new List<SubCategory> {
                    new SubCategory
                    {
                        Name = "App",
                        order = 1
                    },
                    new SubCategory
                    {
                        Name = "Layout",
                        order = 2
                    },
                    new SubCategory
                    {
                        Name = "Sidepanel",
                        order = 3
                    }
                }
        };
​
        var duplicateCategory2 = new Category
        {
            Name = "E-platform",
            SubCategories = new List<SubCategory> {
                    new SubCategory
                    {
                        Name = "Website",
                        order = 1
                    },
                    new SubCategory
                    {
                        Name = "Layout",
                        order = 2
                    }
                }
        };
​
        var categories = new List<Category>
        {
            //APP
            duplicateCategory,
            duplicateCategory,
            new Category
            {
                Name = "E-platform",
                SubCategories = new List<SubCategory> {
                        new SubCategory
                        {
                            Name = "App",
                            order = 1
                        },
                        new SubCategory
                        {
                            Name = "Layout",
                            order = 2
                        }
                    }
            },
            //WEBSITE
            duplicateCategory2,
            duplicateCategory2,
            new Category
            {
                Name = "E-platform",
                SubCategories = new List<SubCategory> {
                        new SubCategory
                        {
                            Name = "Website",
                            order = 1
                        },
                        new SubCategory
                        {
                            Name = "Layout",
                            order = 2
                        },
                        new SubCategory
                        {
                            Name = "Sidepanel",
                            order = 3
                        }
                    }
            }
        };
        
        return categories;
    }
    
    public class Category
    {
        public string Name { get; set; }
        public List<SubCategory> SubCategories { get; set; }
        public override string ToString()
        {
            return $"Name: {Name}, SubCategories: [\n    {string.Join("\n    ", SubCategories.Select(sc => $"({sc.ToString()})"))}\n]";
        }
    }
​
    public class SubCategory
    {
        public int order { get; set; }
        public string Name { get; set; }
        public override string ToString()
        {
            return $"Name: {Name}, order: {order}";
        }
    }
}

View IL Code