Gender
Choose Male or Female. Your choice of gender does not affect your character stats or combat skills.

Build
Select your character's body type. Choose between small, medium, or large. Again, the choice of body build does not affect your character's stats and is purely cosmetic.

Template
Here you can choose whether you want a custom template, or a template inspired by a real superhero. If you choose "custom", you will proceed to customize your template. If you choose "inspired by", you will have the template choices pre-selected, however you will still be able to customize the hero further. The stats and powers of your superhero as well as his or her appearance will resemble the superhero who inspired you. Think of the "inspired by" option as a starting template for your character. The choices for "inspired by" are:

Batman: Hero/Gadgets/Control/Acrobat/Martial Arts
Superman: Hero/Ice/Defense/Flight/Brawler
Catwoman: Villain/Gadgets/Control/Acrobat/Martial Arts
Lex Luthor: Villain/Gadgets/Control/Flight/Hand Blast
The Joker: Villain/Gadgets/Control/Acrobat/Dual Pistol
The Flash: Hero/Fire/Defense/Speedster/Brawler
Wonder Woman: Hero/Mental/Control/Flight/Brawler
Deathstroke: Villain/Gadgets/Control/Acrobat/One-Handed
Bane: Villain/Gadgets/Control/Acrobat/Brawler
Circe: Villain/Sorcery/Healing/Flight/Hand Blast
Beast Boy: Hero/Nature/Healing/Acrobat/Martial Arts
Mister Freeze: Villain/Ice/Defense/Acrobat/Rifle
Green Arrow: Hero/Gadgets/Control/Acrobat/Bow
Steel: Hero/Ice/Defense/Flight/Two-Handed
Martian Manhunter: Hero/Mental/Control/Flight/Brawler

Note the arc to the left of the character. Whenever a sphere appears there, it means more choices are available. Use your mouse wheel or drag the sphere to see the additional choices. Also you can click and drag your character to turn it around and see it from another angle.

Morality
Choose between hero or villain. This determines your allies, enemies, missions, and mentors in the world.

Personality
Choose between Powerful, Serious, Primal, Flirty or Comical. This affects your posture, emotes and expressions. It has no effect on your stats or powers, and is purely for role playing purposes.

Mentor
Your choice of mentor will determine your origin as well as the categories of armor and weaponry that are available to you. Your mentor will also contact you and send you on various missions throughout the game.
For Heroes, the choices are: Batman (technology based), Superman (metahuman) or Wonder Woman (Magic)
For Villains, the choices are:  The Joker (Tech), Lex Luthor (Metahuman), or Circe (Magic)

Power
Your choice of power is a major choice which will determine your abilities, combat strategy, and role in groups. Available choices are: Fire (Defense), Gadgets (Control), Ice (Defense), Mental (Control), Nature (Healing), and Sorcery (Healing)

Movement
Movement affects your speed, style, and maneuvers in combat. You can choose between Flight, Acrobatics, or Super-Speed.

Weapon
Your choice of weapon determines your range, combat speed, and style. Choices are:
Bow (Ranged/Slow/Precise)
Brawling (Melee/Slow/Brutal)
Dual Pistol (Ranged/Fast/Projectile)
Dual Wield (Melee/Fast/Dexterous)
Hand Blast (Melee/Ranged/Fast)
Martial Arts (Melee/Medium Speed/Fluid)
One-Handed (Melee/Fast/Weapon)
Rifle (Ranged/Medium Speed/Projectile)
Staff (Melee/Fast/Dexterous)
Two-Handed (Melee/Slow/Massive)

Now you can customize your Costume:

Body

Skin: Human Skin 02, Leopard. Lion, Tiger, Wolf, Crystalline, Fox, Undead, Chrome, Glowing, Barbarian, Human Skin 01, Lava, Rock, Mummy, Reptile, Plant, Cyborg, Demonic, Robot, Tattooed, Angry, Cheerful, Wise, Youthful, Human Skin 03

Hair: None, Pomp, Liverpool, New Troy, Jimmy, Rockford, Caesar, Afro, Mister B., Spiked Mohawk, Mohawk, Conrows, Happy Painter, Streetwise, The Big Hoff, Castillo, Jules, The Natural, Hyde, Professional, The Hoff, Mobster, Junior, Burnley Special, The Dogg, Racing Stripes, East Ender, Bandit, Bowery, Enforcer, Desperado, Outlaw, Soldier of Fortune, Grappler, Mercenary, The Specialist, Triggerman, Young Gun, Rockabilly, MBA, Philosopher, Chopper, Midvale, Southbank, Cultured, Nottingham, Imperialist, Captain, Bakerline, Ellsworth, Wyatt, Madman, Reporter, Stylish, Inspector, Lackey, Sergeant, Commander, Western Swing, Officer, Holliday, Lawman, Marcus Aurelius, Maximus, Tiberius, Diamond District, Detective, Metalhead, Biker Style, Evil Genius, Wrestler, The Missing Link, Warrior, Heroic, Old School, Roots, New School, West River, Sinister, Dreadlocks, Spiky, Moody, Malevolent, Antihero, Vigilante, Blackguard, Peacemaker, Umpire, El Capitan, Magistrate, Patriarch, Contender, Metro Square, 8th Precinct, Editor-In-Chief, Drill Sergeant, Flattop, Dignified, Glenmorgan, Planet Square, Fade, Mastermind, Kingpin, Challenger, Match, Athlete, Brushed, Adversary, Competitor 

Gear

Head: None, Alien Threat, Biker, Biohunter, Bold Cross, Bold Devil, Bold Domino, Bold Wings, Brave Cross, Brave Devil, Brave Star, Brave Wings, Centurion, Crested Biohunter, Cyclops, Dashing Crusader, Death's Head, Defiant Crusader, Formal, Full Cross, Full Devil, Full Domino, Full Slimline, Full Wings, Future Cop, Gallant Centurion, Gallant Crusader, Half Cross, Half Devil, Half Domino, Half Slimline, Half V Cross, Half Devil, Half V Domino, Half V Wings, Half Wings, Hood, Knight, Masked Cross, Masked Devil, Masked Domino, Masked Wings, Paramilitary, Partial Cross, Partial Devil, Partial Slimline, Partial Star, Partial Wings, Protector, Retro Biohunter, Runed Hood, Skull, Slimline Crusader, Spacefarer, Speedster, Starburst, Street, Thug, V Cross, V Devil, V Domino, V Slimline, V Wings, Visor, Welder's

Face: None, Biker, Bug Goggles, Business, Compound Goggles, Crested Visor, Emissive Eyes, Enhanced Goggles, Eyepatch, Freaky Clown, Full Domino, Gas Mask, Goggles, Half Domino, Incursion, Infiltrator, Metalhead, Monocle, Protection Goggles, Shaded, Sniper, Sniper Goggles, Technician, V Domino, Valiant

Emblem: 1,2,3,4,5,6,7,8,9,10,Animalia, Ankh, Arrow, Atom, B, Bird, Bullet, Butterfly, C, Circled Wings, Club, Cobra, Crosshairs, D, Double Axe, Dynamite, E, Eye of the Horus, F, Fiery Star, Flying Death's Head, G, Grenade, H, Hatchet, Hazard, Horn, Horned Helmet, J, K, King, Knight, L, Leaf, Lightning Bolt, M, Moon, Mushroom Cloud, N, O, P, Paw, Pawn, Pentacle, Q, Queen, R, Ram, Rifle, Rocket, Rook, Royal Wings, S, Shield, Shooting Star, Shuriken, Skull, Snowflake, Spade, Star, Stormcloud, Sun, Swirling Fireball, T, Tornado, Totem, Trident, Turtle, U, V, W, Wings, X, Y, Z

Chest: None, Arcane, Battle Harness, Battle Mage, Biker, Business, Chevron Slimline, Contemporary, Electric, Flames, Flexsuit, Formal, High Collar, Ice, M Slimline, M Suit, Metalhead, Mystic Energy, New Genesis, Paramilitary, Pyramid Slimline, Reverse Slimline, Schoolyard, Shielded Robot, Short Sleeve Slimline, Slimline, Strap Scales, Streak Slimline, Street, T Slimline, T-Shirt, Tank Top, Trench Coat, Triangles, Urban Slick, V Suit

Back: None, Baclpack, Classic, Embellished, Paramilitary, Quiver, Rounded, Short, Small Bird Wings, Small Demonic Wings, Small Tech Wings, Split, Tattered

Hands: None, Banded, Biker, Clasped, Classic, Classic Rivets, Cuffed, Finned, Formal, Lunar, Metalhead, Paramilitary, Power-Reinforced, Slimline Finned, Trim Classic

Waist: None, Biker, Chevron, Clasped, Death's Head, Interlocking, Metalhead, Multipouch, Paramilitary, Riveted, Simple Utility, Square Buckle, Street, Sun-Klasp, Techno

Legs: None, Arcane, Athletic Slimline, Battle Mage, Biker, Briefs, Business, Cargo, Combat Slimline, Contemporary Tech, Elaborate Tech, Electric, Flames, Flexsuit, Formal, Ice, Jeans, Lined Slimline, M Suit, Metalhead, Mystic Energy, New Genesis, Paramilitary, Pyramid Slimline, Reverse Slimline, Schoolyard, Slimline, Strap Scale, Street, Tertiary Slimline, Triangles, Two-Color Slimline, Urban Slick, V Suit

Feet: None, Biker, Business, Casual, Casual School, Chevron, Classic Banded, Classic Slimline, Clean Cuffed, Cuffed, Metalhead, Paramilitary, Power-Reinforced, Schoolyard, Street, Tall Class, Tall Lunar, Tall trim, Trim Cuffed, Urban Slick

Colors

Gear: Choose a 3-color palette, and then customize each part of your gear using those 3 colors.
Skin, Hair, Eyes, Makeup: Choose Color, Intensity, and Brightness

Have fun creating your character! Here is the one I ended up with: Can you do better? Feel free to add a link to screenshots of characters you created in the comments.