While I do agree that changes to the skill system were necessary, increasing the untrained penalty to -4 I don't think is a great solution. So I have this thought, but life has gotten in the way of reading through the forums as thoroughly as I'd like, and if this has been shot down or repeated endlessly I apologize. So here goes:
Has the idea of the proficiency ranks acting not only as gates to new abilities, but caps as well been considered? You could increase the proficiency every level as you do now, but once you reach a certain level, it stops going up until you increase your rank. For example, untrained users may only be able to increase their proficiency rating to be equal to 0, effectively removing any penalty for it. Once you become trained, the cap increases to say +5, not counting any ability score mods or item bonuses. It wouldn't matter if you were level 5 or level 20, you would still only get that +5. Once your rank goes up again to Expert, your cap increases to say +10, and you automatically increase up to your cap or your level, whichever is lower.