There are some limitations. When you get rid of a skill or skill level: 1) You are out some skill points until the skill you got rid of fully goes away and/or 2) You have to regain the mutation level to get something new
Having said that I do agree it's not much of a hard choice, so I might limit it a bit more. However it probably will not be by too much since the player doesn't have much control.
Depths of Peril, Kivi's Underworld, Din's Curse, Drox Operative, Zombasite, & Din's Legacy