One of the issues I've come across in various games is the disuse of average skills. Players generally prefer to use their best skills. The reason is fairly obvious, players want to succeed at what they are doing and so they attempt to solve problems using the skills they are good at.
This habit can lead to a bunch of unused or rarely used skills. While this might lead to a good simulation of a character's actual abilities I feel that it is generally unnecessary to have all those extra skills.