This method is unverified. Additionally, following it through will alter critical game files. Be sure to make back-up files of the files you are altering, or be ready to re-install the game.
If you have no idea what you're doing, or no idea what we're referring to/talking about, do not attempt this hack.
Locate the directory C:Program FilesSEGAAlpha ProtocolAPGameConfig (this is default install path).
Find and back-up the file DefaultLevelChart.ini into something like DefaultLevelChart_ini.BAK or DefaultLevelChart_ini.BACK. This is the file where you will find the AP points you will have, as well as the skill cap maxima.
An example syntax is: LevelChart(MinXPNeeded=0, APGained=30, SkillCap=4, SpecialSkillCap=4)
Alter it to something along the lines of: LevelChart(MinXPNeeded=0, APGained=500, SkillCap=10, SpecialSkillCap=15)
With the above example, you will now get 500 AP points and can max out to skill cap below special skill level. Be sure to save the file as a *.INI file (Notepad will generally allow you to edit INI files) and not as a *.TXT file. Boot the game and wreak havoc.