I can't think of any off the top. If you want to rebook for credit, the screen will ask if you just want to change one leg or both.
I feel like the primary reason people end up with different out and return is because they only had enough points for one direction in one RR account (I have some dates right now because Hubby had enough points for one way and I did for the other), the fares released to different times, or some other reason that forces different bookings. Otherwise, round trip doesn't have any specific draw backs that I can think of.
I'd love to hear if anyone has something I'm missing. I am booking on the next fare drop and would split the reservations if there's a benefit to doing so that I'm missing out on.