Just because the game theorizes something could happen... like the Rogue with Arcana Expertise at level 20 being numerically "better" than a Wizard...
...doesn't mean it ever actually has, does, or will happen.
Talk to me when you actually have a game where there's a Level 20 Rogue PC with a 10 INT and Arcana Expertise standing next to a 20 INT Wizard PC with Arcana, and the Wizard player feels like they are getting overshadowed by the Rogue player. Until that actually happens, it'll just be white room conjecture about the most extremely unlikely scenario that no one should bother wasting their time trying to re-do the skill system just to "fix" it.
If the game only "breaks" when you have to go out of your way to build the unlikeliest of situations that never actually happens... it means the system is actually pretty good. And if by some of the wildest chances this Level 20 Rogue with a 10 INT and Expertise in Arcana DOES appear in your game... my guess is that the story of their time in the campaign will exemplify exactly why they are who they are.