Heh, OK, Mr. Wall of Text. You're right, PvP2 is nothing but rushes, whatever you say. Why not try PvP1 then? I actually prefer PvP1 for a couple reasons - first, I don't have to go pay for a bunch of upgrades, I can buy a new interesting deck for usually under 1500. Second, working with slower pillars forces people to plan ahead a lot more. I've had great success in PvP1 with a huge variety of decks - everything from an Earth/Gravity Shield stall to a novarush to a new Ghost of the Past/Nightmare combo.
Getting back to the ideas... I actually toyed with something like this for a while, but rather than change existing cards I was going to introduce a series of Glyph cards that served as game-wide effects. The Earth glyph, for example, would cause every new creature to gain -1|+2 - both friendlies and foes. I'm not going to give anything else away, though, as the series is still technically in progress - I just haven't got art for it yet.
If you have an idea as complex as this, please, flesh it out more! Only you know what is in your head, and we can all discuss the balance issues more concretely if we have something concrete to discuss.