I use macports quite heavily on my box and while I think it is generally a good system I have a few complaints. [I will add the caveat that it has been a long time since I used apt and similar systems so some of these complaints may also exist for the alternatives...] For starters, ports are frequently out of date. It has reached the point where I am maintaining my own local macport sources tree and hand-rolling portfiles for about 50 packages that I care about and need to be up to date. Secondly, the macports system does not deal well with versioned dependencies. If X depends on a version of Y that is at least rev Z there is no way to express this. You end up just saying that X depends on Y and if there has been an update to Y (which you don't particularly need/want) you are going to get it updated if you update X; this leads to a lot of wasted time for me when some app depends on something like gtk and I end up watching the system pull in the new rev of gtk I don't care about and updates to five other X11 packages. The last minor annoyance is that the tcl scripting system does not handle recursive directory copies well (e.g. copying a doc dir or data dir that has multiple subdirs) so you end up using a recursive mkdir & copy * pattern which will then choke if one of the sub-sub-sub dirs is an empty directory.

Overall, I like the system and use it quite heavily, but it does have some warts.