If they want to keep a similar system it wouldn't be hard to fix.
All they need to do is to separate Character Experience, from Skill Experience.
Let's say you get X amount of XP from an action. That amount would go toward the skill you used and an overall pool of character XP. Skill xp would function the same as it currently does. However you'd also gain an equal amount of XP toward "Character XP." Character XP would be used for purposes of leveling up, assigning focus points, and increases attributes. This would prevent the issue of not being able to level up once your primary skills reached their cap, as even over the cap of the skill you earned "Skill XP" in you would be earning "Character XP" which would allow you to continue earning ways to increases skills caps through focus points and attributes.
It's a really simple fix which would allow you to make specialized characters that had less total skills more more focuses ones, as well as more "jack of all trades" types which would have lower overall skills caps, but a more diverse skill pool.
No offense but if I can see this then surely the people being paid to develop the skill system should be able to as well. If they can't then by all means it's time to lay off some of them and look for outside help. I haven't looked into the game files much myself but I'd suspect this wouldn't exactly be a particularly time intensive change to make. It would also make companions MUCH easier to customize.
Hell I'd even go so far as to say it wouldn't take more than a couple days of work for them to make this a toggleable option upon character creation.