That's basically the main reason why I left MacPorts. The other was the fact that they'd build their own version of already installed programs. The worst offender for a long time was tetex until they finally added support for looking at an existing tetex installation.

I also ran into a number of broken ports. I had used Fink, but I ran into issues with its packaging too. So, when I heard about Homebrew, I decided to try it. It's been pretty decent for me so I've stuck with it. The only major issue I've had has been related to Octave, but that's been a problem for MacPorts too as the OS X version isn't as up to date as the Linux version at times.