Yeah, good catch on the missing abilities.
I'm not seeing the higher CR, though. They stygian aboleth in Lords of Madness is CR 15, and it has 24 Hit Dice! Neothelids, at CR 15, also appear much deadlier. The CR 17 mind worm far outclasses them.
They are definitely superior to the CR 12 ulitharids, though. I could maybe see stretching them to CR 14, but no higher.
Stygian aboleths have no SLAs. Noble aboleths are drowning in them.
[EDIT #1] - You are right, the Stygian is more powerful than the Noble, considerably more so. It is a beast in combat, and defensively stronger (DR 10/magic). SLA-wise it is weaker. Mentally, it is significantly weaker. It is also Gargantuan compared to the Noble's Huge size. Enslavement slightly better with the Stygian, just due to HD. Severely underrated at a CR 15. It would demolish a party at that level. [End Edit #1]
Neolithids are severly underrated (especially with that nonsensical 24 NA).
[EDIT #2] - Ooooph. Neothelid is uber-nasty. If as a GM you had your players face this as a level 15 party, they should have the right to beat you with the DMG. If they succeeded in defeating this thing, your license to run a game should be revoked. This thing should be able to eat Stygian Aboleths for breakfast. The point I am trying to make is that WotC has a terrible knack of assigning crappy CR's. If we use these as a baseline for our CRs, then our creatures will be just as poorly valued. [End Edit #2]
[Edit #3] The one thing I am noticing is that the Noble has far superior psionics and mental scores than any of the 3, making them effective at higher levels. [End Edit #3]
I am not familiar with the Mind Worm. [Found it - Dragon #337]
[Edit #4] Nice creature, a little strange, but nice. Falls in the same realm as the other two, meatier physically, but weaker mentally. In looking it over, it is actually a bit weaker than the Neothelid, and as the other two...under CRed [End Edit #4]
Now granted, this is my opinion based on my experience statting these suckers up for encounters, but, in the end, I cannot concede to using what I perceive as poorly contrived numbers as bookends in evaluating the CR of a monster.
However, in the end, it is my opinion.
Bykov.