I can see two reasons to pick an AIO over an air cooler, none of which has been a concern for me.

1. Using a small case. In a small case you may not be able to fit an air cooler large enough to cool the CPU, an AIO is more flexible and is a great alternative in these cases.
2. Needing to move your computer from place to place. The traditional tower air cooler puts a LOT of strain on the motherboard, this is fine for when the computer is in a static place, but when moving a computer, especially if you are driving, any bumps can cause the cooler to pull on the motherboard, possibly cracking the motherboard. An AIO with it’s smaller footprint is far less susceptible to that. I have a Noctua D15s as my cooler, and if I had to transport my computer in my car I would either remove the cooler and GPU before loading the computer in my car, or lay it down flat.