I'll be going with custom, since that's more fun, and tends to end up with a better character anyway. Feel free to be as general or as specific as you like with ideas.
You can skip all the info below if you already know it, of course, or just want to throw out an idea without working out the details. It's a bit of a long read.Class name: Obvious.
Attributes: Those eight along the left side. If we choose to increase one by a certain amount, we have to reduce others to end up equal. Unless we go with the "cheaty" way of doing things, then we can have whatever we want. They provide various bonuses, and also affect skills related to them.
Strength: Affects damage and weight capacity
Intelligence: Affects maximum amount of Magicka, which is used to cast spells
Willpower: Affects resistance to magic
Agility: Affects chance to hit and avoid being hit
Endurance: Affects hit points, resistance to disease and poisons, healing rate, and fatigue
Personality: Affects how much the NPCs like us
Luck: Affects everything, in a minor way.
Skills: Primary start around 25-30%, major around 20-25%, minor 10-20%, ones we don't pick in the single digits. Levelling is skill based; the game looks at all primary, the highest two major at the time, and the highest minor at the time when it's calculating how close to a level a character is. The choices are (this categorisation is my own, the game doesn't do so officially):
Weapons: Archery, Axe, Blunt Weapon, Hand-to-Hand, Long Blade, Short Blade
Physical: Climbing, Critical Strike, Dodging, Jumping, Running, Swimming
Thieving: Backstabbing, Lockpicking, Pickpocket, Stealth
Magic: Alteration, Destruction, Illusion, Mysticism, Restoration, Thaumaturgy
Languages: Centaurian, Daedric, Dragonish, Giantish, Impish, Nymph, Orcish, Spriggan
Other: Etiquette, Medical, Mercantile, Streetwise
The languages are almost useless; I don't think there are even centaurs or dragons in the game. Orcish, Impish, or Daedric might be useful, but even then not much.
Skill Advancement: Affects how quickly we train up those skills. We don't change this directly; all those buttons to its right (except "Help", of course) are what do it. Lower is better, of course. We have to end up in the area between the "red zones" at x0.3 and x3.0.
Max Hit Points Per Level: Levelling up gives between this number and half of it in hit points. Increasing makes advancement go up; decreasing makes it go down.
AdvantagesParentheses are sub-options. Advantages (and disadvantages) are limited to seven.
Acute Hearing: Not useful for much of anything. Hearing things in dungeons is helpful, but they can be heard well anyway.
Adrenaline Rush: Makes a character tougher when they're at very low health. Often you'll go from too much health for this straight to dead, though it's useful when that doesn't happen.
Athleticism: Reduces fatigue loss from running, swimming, jumping, and so on. Fairly useful if you have the room for it.
Bonus to hit (Animals, Daedra, Humanoid, Undead): Does just that, and also increases damage.
Expertise in (Axe, Blunt Weapon, Hand-to-Hand, Long Blade, Missile Weapon, Short Blade): Increases chance to hit and damage.
Immunity (Disease, Fire, Frost, Magic, Paralysis, Poison, Shock)
Increased Magery: The base is .5 intelligence in spell points; this can set it to 1, 1.5, 1.75, 2, or 3.
Rapid Healing (General, Darkness, In Light): Makes healing go faster while resting.
Regenerate Health (General, Darkness, In Light, Immersed In Water): Allows character to regain health without resting. "Darkness" is a very, very useful one to pick here if you have the space for it.
Resistance (Disease, Fire, Frost, Magic, Paralysis, Poison, Shock)
Spell Absorption (General, Darkness, In Light): Allows spells cast at the character to be redirected into the magicka pool.
DisadvantagesDisadvantages (and advantages) are limited to seven.
Critical Weakness (Disease, Fire, Frost, Magic, Paralysis, Poison, Shock): Very large chance that these take effect.
Damage (Holy Places, Sunlight)
Darkness-Powered Magery (Lower ability, unable to use in daylight): A decent one to pick, since almost all fighting is underground. You don't automatically get all those magicka points back when you go into the darkness, though.
Forbidden Armor Type (Chain, Leather, Plate)
Forbidden Material (Iron, Steel, Silver, Elven, Dwarven, Mithril, Ebony, Orcish, Elven, Daedric): From (approximately) worst to best.
Forbidden Shield Type (Buckler, Kite Shield, Round Shield, Tower Shield): Shields are fairly optional, especially at high levels, though of course that means this doesn't speed skill advancement much either.
Forbidden Weaponry (Axe, Blunt Weapon, Hand-to-Hand, Long Blade, Short Blade): Not a bad idea to pick some from here, since specialising in a weapon or two is the best plan. No Short Blade, though, since we'll probably need that early on.
Inability to Regen Spell Points: A bit of a dangerous one to pick, and I'd rather avoid this, though with "Spell Absorption" it can definitely work.
Light-Powered Magery (Lower ability, unable to use in darkness): Bad idea, since most times magic is used is indoors.
Low Tolerance (Disease, Fire, Frost, Magic, Paralysis, Poison, Shock): Higher chance these take effect.
Phobia (Animals, Daedra, Humanoid, Undead): Lowers chance to hit and damage.
Generally, if they look like they would conflict, you can't use them together. Note that there are a few ways to mess with things, though; one can, for example, take both options under "Darkness-powered magery" and both count to speeding skill advancement, or select "Critical Weakness to Paralysis" as a High Elf and still be immune.
ReputationThis really doesn't affect much, but tweaking it a bit can be fun for, say, roleplaying purposes. Balancing works like attributes do. Increasing reputation with merchants and nobles can have useful effects, though.