Part of the issue remaining is that Proficiency Dice don't offer a significant upgrade to the percent of success over Ability Dice. In other words, a character with 5 Intellect and zero points in Medicine can roll about as well (minus Triumphs) ...
Key phrase: "minus Triumphs". Based on that comment I think you're still thinking about this along only the success/fail axis and discounting the real benefits of those yellow dice. It's true they don't increase chance of success by much, however, and more importantly, they push the average roll from "success with threat" to "success with advantage". Triumphs are just gravy.
Far more interesting narrative things can be done with Advantages and Triumphs than with simple success, and this is what the proficiency dice add. The most important part of this is it lets the player take a lot more control. A Doctor and a Slicer might have the same Intellect, but a Doctor player making a Medicine roll is going to have a lot more opportunity to customize their results than a Slicer player making a Medicine roll. If your players aren't making use of this, then they're missing out on the major differentiating factor.
Anyway, I'm sure a solution can be found for you that will help mitigate the issue without having to restructure the entire game. Some things I've seen on these boards:
- different skill rank costs (above)
- players can only take specs in their careers (i.e.: no Doctor/Assassin)
- make those Talents that reduce setback count by finding reasons to add setback on a regular basis
- upgrade difficulties for untrained use of a skill. I sometimes do this if it seems like failure could be more than unusually problematic, e.g.: somebody untrained in Medicine might cause more problems than they fix; or somebody with no Mechanic skill could break something critical
- tie a rank in a skill above 1 to a minimum row in a Talent tree.