I'm having some weird city enchantment issues since I saved a game last night and came back to it today, most of the unit based enchantments don't seem to be working any longer even after I remove them and recast them.
In my first city I have 15 essence and have Coercion, Nature's Bounty, Meditation, Aura of Grace, Aura of Might, Aura of Vitality and Warrior's Aura. Units I was building were coming out level 1 with none of the city unit trained enchantment bonuses, after recasting them they were coming out level 3 but didn't have extra initiative, defence or hit points.
On new games they were working properly and my older units I made before saving had the bonuses, it was just newer units after coming back to the game via a save which saw the bonuses stop applying to new units.
My general feeling about the city based enchantments is they are fine in general but the first city I find can often have a significant amount of essence around it. Having +45 initiative, +30 defence and +15 hit points is a huge bonus, when the units get them. I guess there is a bit of a opportunity cost because you are sacrificing food and production for them but a lot of them in one city is quite potent.