First, you are wrong about AIs not using essence. They are not great at it, but then, they aren't great at anything much. They will definitely cast the production and research boosters on their first city when they can, and I usually see them use all the available essence in every one of their late game cities. Now, they are not always picking the best spot to settle, but that's something the developers should aim to improve, not throw away.
As for what strategy is added by essence? For starters, tiles without essence are not worthless, especially if you are playing with "Enchanters". In the game I just finished (8 Insane AIs, turn 122 Master Quest win) I had five towns that were settled on essence-less tiles. I used them to claim land, push the enemy dominion back, and ultimately as production facilities. Their production values at turn 122: 112, 126, 112, 112, 140. These are NOT useless cities - they pushed the enemy dominion back, they claimed resources, their grocers and butchers fed the rest of the Kingdom, etc...
Then you have the cities that were settled on essence rich tiles. Those usually become conclaves, and generate mana and research. In the game I'm talking about, I have two conclaves. One is 34 research and 10 mana (without counting shards) and the other is 49 and 13. These usually have little materials, and sometimes little food. To grow, they require food from towns and to build they need cash from taxes and merchants.
And finally you have the cities that fall in the middle. Cities with some essence, that are not tied to a specific role, and where the enchantments are switched depending on what the Kingdom needs. They get "Enchanted Hammers" and "Set in Stone" to get off the ground, they switch to "Meditation" or "Inspiration" when the Kingdom needs mana or research, and they support the specialized cities.
Essence makes cities flexible. It lets the player make choices, and that is, as I said before, GOOD.
Frankly, I do not see your point. You dislike the fact that your starting city is not perfect, and you want to remove one of the resource types so that it is easier to roll a perfect city. I dislike to start with a crappy city myself, and I'd love an option that makes it easy to give everyone a good start. But removing essence is very much not to my liking. Hell, take it to the extreme, and you end up with a simplified, dumb game.