I don't get the generic character levels label. It isn't really important. I get the idea, but not the label.
Either the character is a high level fighter/priest with generic levels or he is a medium level fighter / low level priest with levels in priest and fighter. The problem with this model is that the levels are less defined and as such you don't really have character levels, you have ECL modifiers. Especially notable since options are given to you based on your ECL and not your class levels. I don't think the term generic class level is a good label to put on an ECL modifier.
The negative modifiers for proficiencies are still nonsense.
Either proficiencies modify the chance of producing a fixed bonus to an action, and then a negative modifier is ok. (IE. using support always grant a +2 bonus to the action, but a high level master has a higher chance of granting that bonus than a low level skilled)
Or they have a fixed chance of producing a variable modifier depending on the level and proficiency, and then a negative modifier MUST be avoided. (IE. a high level master gives +6 to the action if he successfully supports, but a medium level expert only grants +2)
I read it as if option 2 is being proposed, am I wrong?
Also, it doesn't make sense to me that a Low fighter/ low wizard that started as fighter can never be as strong in magic as a low wizard/low fighter who started as wizard potentially can be. (Master vs Skilled).
Idea: classes could be remade into proficiencies as well, giving proficiency points for class proficiencies at certain ECL.
You could remove the front loading of proficiencies and then give 1 class proficiency point each 3 ECL. Each class proficiency point could then be exchanged for 3 class specific proficiency points. And proficiencies outside of the class would then cost double.
Some proficiencies like agitate might be on more than one class list.
So a fighter could get espionage or assassination proficiencies while delving deeper into his fighter class and unlocking his fighter bonus actions. But the cross class proficiencies would cost him 2 points for every one advance. Or he could delve deeper into his warcraft and contest or rule law proficiencies at no negative penalty. Or he could multiclass to wizard gaining 3 wizard proficiency points to spend on wizard stuff.
That would remove the problem with the fighter/wizard from above. But it would require a near complete remake of the proposal since it would raise other issues