I agree with PigeonPigeon.
Customisation traits should include some extreme, game changing traits as well as bland ones. So you can go for a balanced or specialist sovereign. You should also be able to go for a 'vanilla' sovereign, with no special disadvantages or perks.
Also, custom traits should be UNIQUE. Why start with an 'extra' spell that everyone else will have in a few moment. A UNIQUE spell or technology that cannot be found any other way, that is worthwhile.
The Ring of Fire - player begins the game with an artefact left over from the war that can cast the volcano spell. It begins the game charged with a single use. Enough to strike a huge blow against a single enemy player, but not to win the game.
The Last Seed of the Tree of Joy - before the Titans devastated the world of Elemental nature's verdancy was focussed in the World Tree. In the war the Tree was destroyed. The Last Seed can be planted on a tile in a city. The tile becomes equivalent to a an epic farm. In addition it gives bonuses to fertility, prestige and mana income. The player also gets a one-time bonus of 2 essence.
LIFE - Attendant Light - The Forces of Light enable you to summon a divine creature of light to attend you. The power of the creature is proportionate to your essence (i.e. grows in power with summoner, valuable throughout game). You can only have one of these creatures at a time. Power is equivalent to a dragon, depending on the cost of the perk.
DEATH - Demon of Lust - The Forces of Darkness enable you to sommon a lascivious demon of darkness to attend you. The power of the creature is proportionate to your essence (i.e. grows in power with summoner, valuable throughout game). You can only have one of these creatures at a time. Power is equivalent to a dragon, depending on the cost of the perk.
FINER HEALING - The sovereign gets a healing spell that gives better HP / mana than any standard spell. Only the sovereign can cast it, not their heroes.
Fey Friend - Can periodically recruit fey creatures. Cost varies (i.e. more powerful units become available as the game progresses). Vary from tiny fairy scouts to ents.
Child of Darkness - Is the child of a dark titan and gains the power to cast a death spell on mundane units once per turn. (Overland turn, so if three combats in a turn, can only use the power in one). Mundane units wounded in melee have a chance of dying. People are terrified of the sovereign and they suffer a massive prestige penalty.
Cripple - Your character has only one hitpoint and they cannot be raised but gets double essence per level though. This gives you magical power to burn but forces you to play as a sorceror king enchanting minions, not as a Sauron.
Heroic - Your character killed a monstrous creature early in his career. Huge prestige bonus but very small chance of recruiting magical creatures.
Dark Pact - Before the game began, the player made a pact with a demon. The player begins with DOUBLE essence (but gets normal increase per level). HOWEVER the player must one day repay his debt. Essentially, at some critical point in the game the player's population AND armies are reduced in size by 10-90%. Ideally this should always be at an inconvenient moment, like after declaring war on another player. The catastrophe is one shot ... once it has happened the player does not have to worry about it a second time.