for the loss of 48% chance to get 1 rare seems quite desirible trade
That's incorrect math. You can't add probabilities on top of one another like that. If this were valid, you'd have a 520% chance of drawing a Common card. ;)
The situation that makes Wish useful is the same reason that you wouldn't want the chance to draw a Common card to decrease while the game goes on. For many decks, your hand can grow stale as the game goes on and as you accumulate cards that don't function well against your opponent's strategy. Or worse, your opponent has employed a deck that reduces your resources and/or facilities, and you're stuck with a hand of expensive cards you'll never have the opportunity to play. In both cases, refreshing your hand is a blessing, and the right Commons are going to help you out of your rut. (And if that isn't the case, one should reevaluate which Commons were selected at deck creation.)
The draw chances are known (at least to players who've read the manual), and making the mechanics more complicated wouldn't benefit the game, especially for new players. It's a lot easier to look at the trio of percentages than it is to interpret a graph or an algebraic formula...