I believe handling of .pacnew files should be handled automatically. I recently had a problem with dhcpcd failing on boot and it turns out there was a .pacnew file for it in /etc/conf.d/ that had the fix which i totally forgot was there...So i have 2 proposals:

1. Include a .pacold file with packages when a conf file changes (or requires a .pacnew), if the old config file (say dhcpcd.conf) matches the .pacold (dhcpcd.conf.pacold), meaning the user hasn't changed it, remove the old dhcpcd.conf, remove the .pacold file and automatically rename dhcpcd.conf.pacnew to dhcpcd.conf so people who don't change some of their .conf files don't have to deal with it.

2. When a .pacnew comes in on a package upgrade, do what debian does and throw up a menu asking: 1. Look at the difference between the 2 files (uses diff -u old.file new.file > less and dumps back to this menu on exiting less), 2. replace current with $file.pacnew, 3. keep current, remove $file.pacnew, 4. edit $file.pacnew and replace current with it.

I think one of these outcomes would make it much easier for new users and people who don't edit all their .conf files alike to have fewer issues.