I'm seeing this problem, too, and it's a BIG PROBLEM!
I teach computer science at The University of Arizona. I often want to paste code onto a slide. With PowerPoint for Mac 2011, that works fine. With PowerPoint for Mac 2016, multiple lines are squashed onto a single line, completely
ruining the layout.
Although I see this squashing text pasted from Aquamacs 2.4 and iTerm 0.9.6, I've found that text pasted from Terminal 2.6.1 and TextEdit 1.11 does not exhibit the squashed behavior BUT blank lines are doubled.
Here's a bit of a workaround--the following pipeline takes the text on the clipboard, converts it to RTF, and then puts it back on the clipboard. Line breaks are preserved, but empty lines are doubled.
pbpaste | textutil -stdin -stdout -convert rtf | pbcopy
Here's a shell script, with an embedded Python program (2 or 3), that seems to avoid the empty line doubling. I'll show it with cat:
% cat ~/sbin/ppt-paste
pbpaste | python -s <(cat <<X
import sys
sys.stdout.write(sys.stdin.read().replace("\n\n","<p><br>").replace("\n","<br>").replace(" "," "))
X) | textutil -stdin -stdout -format html -convert rtf | pbcopy
If you don't know how to work with scripts, here's a simple way to use it: First save it as ppt-paste in your home directory. Then, start up Terminal. Switch back to whatever app has text of interest and copy it to the clipboard.
Switch to Terminal and type 'bash ppt-paste'. Switch to PPT and paste. Repeat as needed. Note that up-arrow in Terminal recalls previous commands, so no need to type 'bash ppt-paste' every time.