Any reason to use auto-implemented properties over manual implemented properties?

There are people who think that automatic properties can be somewhat evil but apart from that they are just syntactic sugar. You don't gain anything by using them apart from saving a few lines of code and you can potentially create more work for yourself (by having to implement it manually anyway later on because you want to do some checking or raise an event). Consistency is quite valuable in programing (imho).

Auto-implemented properties are not guaranteed to keep the same backing field name between builds. Therefore, it is theoretically possible that serializing an object in one version of an assembly, and then re-serializing that same object in another assembly could cause breaking changes.

This is highly unlikely, but it is a valid concern if you're trying to maintain the ability to "swap out" version of your assemblies for newer versions.

By using manually implemented properties, you're guaranteed that the backing field never changes (unless you change it specifically).

Aside from that minute difference, an auto-property is a normal property that is implemented automatically with a backing field.

It doesn't grant you anything extra beyond being concise. If you prefer the more verbose syntax, then by all means, use that.

One advantage to using auto props is that it can potentially save you from making a silly coding mistake such as accidentally assigning the wrong private variable to a property. Trust me, I've done it before!

Your point about auto props not being very flexible is a good one. The only flexibility you have is by either using private get or private set to limit scope. If your getters or setters have any complexity to them then the auto props are no longer a viable option.