I don't think moving marked units from core to special or from special to rare would be right, because we'd already pay the price in points. I don't like limiting the number or markable units aswell
Ok, this is my attempt on marks. I know it probably needs more balance, that's just to show my ideas. Please notice that "blessings" are only available for characters, and they should cost way more then the standard marks. They are cumulative with the mark unless otherwise stated. Characters cannot have a mark from a god and a blessing from another, but they can join units with different marks even if they don't get (or give) additional benefits from marks they didn't pay for.
Chotec: attacks count as magic and flaming. Blessing: at the end of the phase roll a D6 for each successful wound inflicted by the blessed character: on a roll of 5+ Chotec’s fire consumes the foe and the target suffers an automatic wound with no saves allowed. These wounds cannot generate additional wounds.
Sotek: skinks only. The marked unit gains poisoned attacks and hatred (skaven). Poison works on a 5+ if the unit already had poisoned attacks. Blessing: Sotek’s poison pervades the blood and scales of the blessed character. Every time an enemy hits the blessed character in close combat roll a D6: on a 6+ he suffers an automatic wound. Every time the blessed character suffers a wound his poisoned blood hits the foes: the enemy models in base contact with the blessed character take a toughness test with a penalty equal to the number of wounds suffered by the Sotek’s champion during the phase: if they fail they suffer D3 automatic wounds with no armor saves allowed.
Quetzl: +1 scaly skin and toughness. Blessing: the blessed character gets an additional +1 scaly skin and toughness, as long as a bonus wound
Tepok: the blessed unit counts as an arcane vassal. Blessing: a blessed wizard gains an additional magic level. If the wizard has the loremaster special rule or if he doesn’t generate his spells in the usual way he adds an additional D3 to his casting and dispelling attempts. If the wizard has the arcane vassal special rule he can channel every kind of spell. If the blessed character has not wizard levels he gains an innate bound spell called “Tepok’s Riddle”
-Tepok’s Riddle: innate bound spell, power level 10, evocation. If successfully cast place a clone of the character within 3” to him or in base contact with him. This clone is identical to the character and has the same items, but his magic items count as mundane items of the same kind. The clone has the Ethereal and crumble special rules in addition to all the special rules the original character may have, and comes into play with the amount of wounds the characted had when he casted the spell. Note that if the character successfully casts the spell again in the next magic phase his clone will duplicate aswell as him, and so on. Killing the real character will destroy all his duplicates.
Tzlatcotl: the blessed unit gains the stubborn special rule, or unbreakable if already stubborn. Blessing: after being reduced to 0 wounds or less but before removing his model the blessed character can choose to lose an attack or a wizard level to come back with one wound. All the attacks or wizard levels lost in this way cannot be recovered and the character dies if his attack or magic level value reaches 0
Huanchi: the unit gains +2 movement, swiftstride and devastating charge. Blessing: characters gain an additional +2 movement and can choose to disengage a fight. Even if this is not a flee the opponents can pursue unless they’re still engaged in close combat
Itzl: predatory fighter units only. PF on 5+, frenzy. Blessing: reroll failed hits and PF attacks can generate more PF attacks. A mounted champion of Itzl can force his opponents to attack him instead of his mount
Tzunki: the sacred waters of the spawning pools still flow in the veins of these fighters. A the end of each player turn the unit recovers a number of wounds equal to the result of a D6. Units cannot exceed their starting number. Blessing: a Tzunki champion loses the mark benefit but gains the regeneration special rule.