I´m surprised to see three pages without counter-arguments.
I´ll give you some.
First, we should see, what the handicap would measure. It measures how often the cards are drawn. But does this directly show, how popular a card is ? No! Only partial.
An example:
Dimensional Shields are often used in chains. If a deck has a Dimensional Shield, it probably has more than one.
The same thing could go for other cards like Devourer, attacker in mono/duo decks...
Other cards are only a few times in decks like Weapons (if not flying) or Shields except Dim Shield, Wings (or Sundial, if you´d see it as a kind of shield). Decks normally don´t have more than 2-3 Shields of one kind.
An number example
Deck1 Deck2 Deck3
Numbers of Dim Shield 6 0 0
Numbers of T. Shield 1 1 1
Total:6 Dim Shield, 3 TowerShield -> Dim Shield more popular -> Higher handicap.
Although all decks in the example have a Tower Shield, and this card should be seen as more popular.
Another counterargument is that the handicap system makes deck building quite mathematical and dependent on rating of cards.
So I´d vote NO.
I don't think the system would measure how many times a card is drawn, but it would examine the deck codes everytime a duel starts.
From deck codes you can know how popular is a card, even if it isn't drawn in that specifical match.
Also, there will be neutral cards that would not give handicap, and there will be unpopular and popular cards that modify your handicap consequently.
Also, this system has been suggested only for the Arena, and only for submitted decks, to promote innovation and originality.
The rest of the game, even the deck you use to grind arena, would be unaffected by handicap.
About deckbuilding becoming mathematical, you shouldn't bother about that: if you submit a mainstream deck (Firestall for example!), it will win anyway, but give less electrum for that. Right now Arena gives 5 electrum per match, so i don't think it's a big deal!