I'm a big fan of IntelliJ, I'm not sure I agree w/ this - though it might be specific to your use case.
Can you note some specific features that are missing? I understand if one application requires a different way of doing something, but that doesn't necessary mean that functionality is missing or different.
One big set of features missing are the configuration options available in PyCharm. For example being able to configure Vagrant in PyCharm provides its own UI in the IDE settings. I have created a screenshot showing all the various PyCharm setting views compared to IntelliJ with the Python Plugin installed:
You can actually get some of the Vagrant features with a separate Vagrant plugin in IntelliJ, but PyCharm lets you set up the Python interpreter with Vagrant via a really nice UI.
Of course, that makes sense. That feature is under the Remote Interpreter in IntelliJ. Vagrant configurations can change between modules, which is why it's organized under IntelliJ under module settings -> SDKs.
So that falls under "hidden under a different area" in the IntelliJ project, not missing functionality.
The concept of modules in IntelliJ is not in PyCharm, I believe. Though, I could be wrong.
Can you note some specific features that are missing? I understand if one application requires a different way of doing something, but that doesn't necessary mean that functionality is missing or different.