I'm not sure if you know about this but PermisisonsEx does not support the creation of, if it is still like this, the creation of more than 16 groups. It is also one of the few permission plugins that can hook into Multiverse-Core's world aliases and display them before the group prefix.
There have also been recent reports of, upon doing the reload command in the console, PermissionsEx omits permissions assigned to your groups. For example, if you had the permission - -bukkit.command.plugins so a player could not perform /pl there is a slight chance that PermissionsEx will omit that command and allow players to perform such command when reloaded from the console.
I'm not saying you shouldn't use PEX but as someone who had been hosting since 1.2.5 I find it to be a very serious problem. In my own opinion I would suggest using Essentials Group Manager as it is more friendly with other plugins and the hierarchy of groups is easier to create and understand (when you have groups with more than 100 permissions if not using global groups in your groups.yml).
