Regarding the question of Pure Mortal +2 bonus remaining balanced as base refresh changes:
I agree, and I think it's a more general problem with the concept of having power modifiers in the form of adders. I don't like how the Catch adder works with that Toughness powers, either.
One answer to this (for Pure Mortal, at least) is to just accept that mortals, regardless of skill, cannot and should not compete on even ground with powerful supernatural creatures. Of course, this basically means that the players of such characters need to (a) build new characters, or (b) switch to supernatural templates, both of which would mean they don't get to play the character they chose.
Another possible way to deal with this (through house rules) might be to scale the pure mortal bonus. Instead of treating it as a straight +2, treat it as (for example) a +1 bonus per 4 base refresh. So once the game's base refresh hits 12, the pure mortals would increase their bonus to +3, and so on. On the other end of the spectrum, a pure mortal in a "Feet in the Water" game might only get +1 refresh, increasing to +2 once the game reaches 8 refresh.