Groups and permissions are fixed (hopefully). Furthermore, checking one's powers via /powers player [player] now shows powers that player has gained from their group and permissions.
The power options system (pConfig) has been slightly overhauled:
The backend system has been parameterized. This translates into a slight performance boost.
Option values are mostly stored internally, meaning it doesn't need to constantly get values from a given power's config file (which also means better performance).
The frontend is also improved: /powers power [power] -o now shows a list of all options along with their current value. The other information (description, type, and default value) can be viewed with the command /powers power [power] -o [option].
Attempting to view powers that aren't enabled will now temporarily enable them for viewing purposes. Previously, doing this made it impossible for powers to populate their descriptions since this info came from their options, which couldn't load while the power was disabled.
If the server isn't using an official Bukkit build, it'll attempt to use other methods to identify the server's MC version (this is possibly why MCPCPlus wasn't working).
When an error occurs while using the custom plugin manager and/or scheduler with error printstacks on, it will identify the class and line number that caused the error. This is to counter generic errors (e.g. Task #180 caused an exception).
A given server will now only email a given error once per session. During v4.3.1 I received errors as many as five per second, most of which were duplicates presumably from the same servers, causing unneccessary lag.