Apple mail unable to reply or close windows
In my case the following approach has fixed this issue, for the time being at least:

(Using Mail.app version 9.2)

Go to Mail > Preferences and select the 'Composing' tab. In the section of preferences relating to 'Responding' and change the settings so that they are the opposite of what you normally use. Save the changes.

I then quit Mail. (In my case I then restarted the machine as well - for a wholly separate and unrelated reason, but I don't know if that's a critical step or not, certainly won't do any harm.) Re-launch mail, and I found that replying to a message now conforms to the new preferences that I've set.

I then re-edited the preferences to set them back to what I wanted. Tried a new reply, and it works - the target addresses are in place, the text of the original is there and quoted.

I guess the issue may have been due to the original preference settings getting corrupted in some way. I'll keep it under review, and if it stops working again anytime soon, I'll aim to add a comment here.