Skill systems from the start was meant to be a foundation to build your own skills off of, and as such, there was no attempt to balance the default skills. Skill systems also heavily took skills from Fates and Awakening, a game where the norm was player units having six skills and generics having one or two. Many people who used skill systems tried to replicate how Fates and Awakening skill systems worked in in their FEGBA hacks.
Trying to keep some balance while giving every player unit six skills from an intentionally unbalanced skill list was hard enough, but the real annoyance was enemy generic skills. Even Fates showed a lot of restraint when putting skills on generics, only having one or two on specific generics on harder difficulties. And unlike FEGBA, Fates had the UI to easily check skills at a moment’s notice. Playing in a FEGBA environment where generics consistently have skills makes you feel as if you’re in an information deficit, always one or two math problems away from fully understanding how the units will interact with each other. It got to a point where well respected members of the community would disparaged skill systems in it’s entirety, tired of losing units because they forgot Elbow Room existed. As you would expect, it hampered the desire of a lot of people to use skill systems.
That being said, some hacks do use skill system for its intended purposes. Cerulean Coast by Rivian has unique, high impact skills that use SkillSystems without using the default skill system skills. And, while not SkillSystems™, and majority of LT games currently have a skill system.