ALFA has overhauled the skill system in NwN2 to comply with the skills presented in Pen and Paper. Information on skills and how they work can be found at the d20 System Reference Document here:
http://www.d20srd.org/indexes/skills.htm
Those skills which were used in NwN2 which do not exist or work differently in PnP have been dealt with as follows:
Craft(Any) - These skills can still be used, but will require the assistance of a DM.
Lore - The lore skill was an aggregation of all the Knowledge skills, and as such is considered to have been broken up into the variety of Knowledge skills that exist now.
Parry - Parry can still have ranks put into it and can be used as normal.
Perform - Perform has been broken up into individual categories. NOTE: There is currently a bug with Perform skills not properly allowing for the use of Bard abilities. To avoid this bug, follow this process at character creation:
Do not put ANY skill points in ANY perform skill in the character creation; instead, dump those skill points you want for perform skills into something else. Once you have clicked 'finish' and logged into the game, youll be prompted to finalize skill points or to adjust skill distrubutions - NOW is when you adjust your skillpoints. Remove the skill points you placed into dummy skills using the prompts, then place those points into your desired perform skills. Viola!, your bard should now be working properly.~Heero
Set Trap - This skill has been removed from ALFA along with the trap kits to which it applies.
Taunt - This skill has been removed from ALFA.