Well, module management for one. Php modules are not great.
Discussion
I assume importing libraries. I think autoloading works greats, loading only what needed. What are the downsides in your opinion?
No, I mean importing other modules. Just the fact that you have to specify that a module should only be imported once ("require_once") or it will attempt to redefine things in a circular import illustrates the problem. Python has a similar problem here.