I think that if we are going to give Lorgar any mutations it should be things that enhance and work with his other skills and abilities, are magical in some way so that he has the excuse of them being more weird magic and importantly, things he can turn on and off at will. Here are some examples I can think of:
Gaseous Form
6 Points
The fomor is able to reduce her body into a gaseous state, taking only one turn to make the transformation. She can then glide through the air at her walking speed. While in gaseous form, she cannot be harmed by kinetic attacks (fist, swords, etc), but electricity, fire, and radiation will still affect her. Also most mental and mystical attacks will still affect her (except those involving eye contact; Storyteller's discretion). The gaseous form holds together well even in a strong wind, although the
Gift: Cutting Wind will still harm her. There is usually a horrible stench in this form.
System: The fomor must spend a point of Willpower to become gaseous, and another to become solid again.
The smell is not ideal but being able to become gas means hr would be able to squeeze through tight spaces, hide as a thin mist etc... Basically all that vampire stuff every D&D party is scared of only now it's a nine foot tall Demigod with magical martial arts. Also given that Lorgar can just naturally exist in space without harm he could ever use this to creep over the hulls of enemy space ships and sneak in the moment there is a breach.
Phoenix Fire
5 Points
The fomor can self-immolate, becoming a walking bonfire. The flames do no damage to the fomor, but will ignite any flammable item they touch (exploding ammo, anyone?), and may also set fire to any building the fomor is inside.
System: The fomor spends one Willpower point and rolls Stamina + Occult (difficulty 7). The flames are considered a raging chemical fire (three Health Levels of damage; difficulty 9 to soak). The effect lasts one turn per success
If he is going to fight with his fists anyway being able to set himself on fire would be quite nice, good for his legend too seeing as many cultures have 'fire purifies' as part of their beliefs. This looks like pretty basic pyromancy, but isn't, he is not touching the warp and it does not cost him a willpower to use it
Shadowplay
4 Points
The fomor can manipulate the shadows about him, and pull them together into a globe. Most people will be unable to see through this dense shadow. Minor use of this Power can add to the fomori's Stealth rolls, as well as Intimidation. The fomor is always able to see in his own shadows.
System: The fomor rolls Wits + Stealth (difficulty 6). The effect lasts for one turn per success, unless a Willpower point is spent; in which case, the effect lasts for one scene. The total radius that can be manipulated is 15 yards.
This does not fit as well with his mythos, but there's some space in there via TDC, the fact that he can always see through his own shadows is also useful obviously
Shapechange
Varies
The fomor is able to transform his body into the shape of a something else, such as an animal, or even another person.
System: The fomor spends one Willpower point and rolls Stamina + Athletics (difficulty 6). Transformation usually takes one turn, although the nature of the change may dictate a slower or quicker shift. The fomor can shift back into his "natural" form at will. Any clothing, equipment or weapons should be discarded first unless the new form could carry them as well.This Power only grants the ability to change shape. Any non-human characteristics of the new form must be purchased with the appropriate Advantages. If the fomor were to shift from human form into a white falcon, he would also have to purchase Wings, Claws, and reduced Size, regardless of which form was his real one.
This is I think the most interesting power since it would synergize with Clark Kenting on everything from stealth to going incognito among his subjects.