Python
I know you'll hate me for saying this, but Python is a mess. I love programming in Python, but holy crap-a-reno is dealing with all the modules a pain-in-the-ass-a-who. Then python 3 came out. Now I have a complete mess of modules on my machine. I have some modules that are system wide and others that are install just for me. I have no idea how it got so screwed up. It's probably that my Mac is 6 years old and it's just been a slow module death. I'd love to wipe it all clean and start over. I think that would just make it worse.
I'm sure there is some logic behind it, and I'm sure all the python pros are laughing, but getting python working for the average user is nuts. I'm trying to walk some people through it now and it's just impossible.