Make the abilities spec specific. This way you gain access to all the interactions in the base kit of each spec and can even account for interactions with talents.
Integrate the abilities into the core playstyle and kit of the spec, committing fully to creating 4 sub-specs for each spec that play noticeably differently. Think Clarity of Power Shadow vs regular Shadow in Warlords of Draenor or 2h vs DW Frost for most of their existence. Maybe even add a passive to each Covenant as well as the class ability in order to hammer home this playstyle difference.
Now there’s no reason for any ability to be in any of the 4 Essence categories anymore. However, this would likely be a balancing nightmare because you now effectively have 144 specs instead of 36, and they’re struggling with “just” 36.
An alternative would be to go with the option that’s such a popular suggestion across the internet that Wowhead built it into their talent calculator: turn Covenant abilities into talents. This way you avoid the problem of 75% of people not being able to use them, and can thus treat them more or less like regular talents in terms of impact on how the spec plays or what niches the spec has access to. This would still require changing the abilities to be spec specific, but not necessarily as transformative as the full on subclass option.
