EYE, captain!
The more I think about it,
detect thoughts is just wrong, wrong, wrong. There is no indication whatsoever that it can read people’s minds. What it does have is a sense of the immediately future. It knows what someone is going to say, not because it can read their mind, but because it can read the future. If a person says “attack this thing from the back!” then the Eye knows what it is going to do ahead of time. If the person says no such thing, then the Eye would still know that someone was going to attack, because it would “see” the attacker before he attacked. A lot of the combat application of this power is in the insight bonus to AC and the uncanny dodge power. I could see giving it an insight attack bonus as well. As for the knowing what someone is going to say, if there is no appropriate 3.5 ability for reading the future then we should just make that flavor text and stop agonizing over it.

so, detect thoughts is officially out.
These spell-likes were being worked on before, but we kind of left off with them:
Spell-Like Abilities: The following abilities are always active on the Eye’s person, as the spells (caster level 12th); clairaudience/clairvoyance, detect magic, find traps, and true seeing. They can be dispelled, but the Eye can reactivate them as a free action.
Also, since “it cannot be surprised, as long as it is awake”, is there a way to make it immune to surprise, or would making immune to being caught flat-footed like the Hand keep it active during a surprise round?
Shade said:
Alertness and/or Improved Init as bonus feats, racial bonus to Spot and Listen, or even an insight bonus to initiative, Spot, and/or Listen could cover this as well.
Should we give it low-light vision and darkvision? All-around vision? Blindsight/sense? An additional Search & Spot bonus? I can’t see giving it bonuses to listen checks, actually.
There is really only one big issue left to resolve, and that is the psychic tracking sense power. Here is the original description, as a reminder:
Vecna Lives! said:
The Eye's primary purpose is as a psychic tracker for the priests of Vecna. Once the Eye has seen an intelligent being – either directly or through scrying - it can sense that creature's aura over large distances. The range depends on the abilities of the player character. Those with no spellcasting ability can be detected only within a one-mile radius. Those with any spellcasting abilities are detectable at a radius in mules equal to their spell level. Thus a 12th level wizard (who is able to cast spells up to 6th level) is detectable within a six-mile radius.
The Eye's tracking ability is not infallible. Large concentrations of magical energy can shield a target's aura. Artifacts, stockpiles of magic items, or even areas with a high preponderance of spellcasters all have this effect. For example, simply entering the Guild of Wizardry is enough to block the Eye's tracking sense. In doubtful cases, the Eye must roll a successful saving throw vs. spell to retain the "scent."
Here is what we had so far:
“Tracking Sense” (Su): The eye has the ability to sense an intelligent creature’s aura over long distances, if it has seen the creature directly or through scrying. The Eye can detect most creatures up to 1 mile away. Creatures with spellcasting abilities are detectable at a range in miles equal to their total caster levels (or, like the text, a number or miles equal to the highest level of spells they can cast?).
To track a creature’s aura, the Eye must succeed on a DC X (knowledge arcana? Gather information? Search?) check. If it fails the check, the Eye can retry after (1 hour) of meditation. If successful, the Eye can sense the creature as if by the locate creature spell.
This tracking ability can be blocked if the creature is within X feet of a large concentration of magical energy, such as an artifact, a stockpile of magic items, or at least (three?) other spellcasters. In such an instance, the Eye must succeed on a DC X Will save or lose the ability to track the creature’s aura until it leaves the source of magical energy. Running water does not block this ability.
Shade said:
Caster level is probably a good idea, as it helps with those situations where a creature has a spell-like ability that doesn't mimic a specific spell. I'd go with the Search check. Go with the standard 30 feet for the "large concentration of magical energy"?