Mail - Reply from the same address the message was sent to
I recently switched from using Gmail's web interface to Apple Mail. I maintain multiple email addresses, and have been having one particular issue with Mail that was easy to solve in Gmail. I have a university email address, say name@uni.edu. My university's department also gives me the email address name@dept.uni.edu. Unfortunately, the department-specific email address only has POP access available. I do not like using POP since emails read on my phone cannot be marked as read on my computer. When I used Gmail, I simply forwarded the dept.uni.edu email address to the main uni.edu address. I set up a "Send mail as" address in Gmail so that I could send mail from the dept.uni.edu address. I then checked the "Reply from the same address the message was sent to" box, and everything worked like I wanted. Mail sent to name@dept.uni.edu was forwarded to the uni.edu address (which has IMAP support), and if I tried to reply, Gmail was intelligent enough to automatically reply from the dept.uni.edu address when appropriate.
I have found Apple Mail, however, completely counterintuitive. There seems to be no way of doing this, that I can tell, without manually specifying the outgoing account. I currently have set up two separate accounts for the aforementioned email addresses, and switch the "From" address as needed. Is there a solution to this? It's somewhat disappointing that Gmail's web interface is so much more intuitive than Mail, as this is by no means the only problem I have encountered (just the only one I cannot find a solution to elsewhere). This is all using Mail 6.1 on OS X 10.8.2.
Mail-OTHER, OS X Mountain Lion (10.8.2)