*Improving* skills over the cap penalty is 5% per skill over the level, to all xp spent for all skills, including the existing ones. So 1 or 2 skills over the cap isn't TOO harsh, but more than a few does get pretty expensive.
Some of the ways around this were:
- you can DROP skills that were useful early on, or that you wanted to try out, but not so useful in the later game, like maybe Survival, Performance, Pick Pockets, Dominate Animal or even Shopping or melee skills. Investigation and CodeBreaking once you're past the campaign bits and missions where they're useful.
- really focus on knowledge - I liked having lots of skills, so most of my characters had knowledge about as high as was feasible
- take the trait that gives you more free skill slots - multiple times if needed.
- just eat the penalty for late game skills. Get all the others up to the useful max (the level gains get PRETTY damn harsh at high levels, so you'll hit a point where the next level is too much work to reach). 20,30,even 40% penalty on a few skills isn't unsurmountable, especially if you don't have to get them as insanely high as you liked Mecha Piloting (Cybertech, Leadership, Robotics)
Here's the text from the wiki:
"Each skill is linked to one of your attributes, and the combined scores are checked when a skill is used in the game. There is a limit to the number of skills your character can learn based on their Knowledge attribute. The formula is (Kn * 120%) + 5, so a character with a Knowledge of 10 can learn 17 skills, e.g. (10 * 120% = 12 + 5 = 17). If you go over this limit then the amount of XP needed to raise all of your skills will increase by a fixed factor; first 5%, then 10% (of the original 100XP) for each extra skill, which can quickly make your existing skills much more expensive to improve."