Idea 2 is what I think they will do.
1 and 3 will ruin the game for both, the players and devs.
If you give players such a simple way to complete getting all the cards out there, then there is nothing to play for and nothing to pay for.
Magic is not balanced this way with a card upgrade system and this would be awful.
Also: new players would get pooped on constantly and players who have had the benefit of the rune card packs will be unstoppable.
Also, that would make uncommons WAY better than most rares and mythics.