To Start: Yes some adjustments would have to be made for this to work, I understand that. I think that this could be a simple way to add more diversity between classes and give both PvE and PvP some interesting yet simple benefits while keeping the current talent system unaffected.
I'm Not saying to change the Talent system, this is merely an extension
Synergy Tree: This tree is Universal between all classes and races and would function in a similar fashion to the old school talent tree without any gating. It would give a very basic way to differentiate your character using Resistances(including physical).
What it does: The Synergy tree would allow you to gain specific resistances(including physical) based on the statistical value of your primary stat without any deductions to that stat. Your decision would have to be made carefully as you would have to weigh which form of damage you view as the most threatening to you because you can either have 1(maybe 2) strong resistances or be a jack of all resistances.
How this could affect things: In PvE we would get back resistances without that god awful gear grind and if you could save synergy specs and switch through them in similar fashion as Talents and Specs it wouldn't be any more of a bother.
In PvP players have more of an ability to self balance a game. If players know that a class is OP or in general incredibly potent against them they could Synergize towards defending against that at the cost of course of making other classes more potent..
Some Homogenization is fine so long as it makes sense, in WoW it took quite a few years before classes other then rogues learned how to run.