Because talented deck builders would be disadvantaged because they would lose more points for a loss. Weak deck builders will have an advantage because they lose fewer points for a loss.
Deck building is a big part of Elements. Good deck builders are usually good players. However, you are causing good decks to lose more points for a loss, thus good deck builders lose more points for a loss, thus good players lose more points for a loss, and thus good players are disadvantaged like I said earlier.
Why do you want to handicap good players?
EDIT: OK, I decided to include a suggestion. How about the deck is rated by how many upgraded cards it has. For example, no upgrades would be AI1. Up to 25% upgrades would be AI2. Up to 50% is AI3. Up to 75% is AI4, and up to 100% is AI5. This way you still have the AI system, but talented deck builders that use few upgraded cards will have a low ranking and be rewarded for their talented deckbuilding.
Not trying to be mean or anything here, but here's a different version of the same rules.
Every person builds a deck. Organizers rate it from ai1-ai5. For every win, you gain points based on the ranking of your opponent's deck. For example: I defeat an ai4 deck, I get 4 points. This is so people who continuously "grind" off of ai1 decks will not have as high of a score as people who grind against ai5 decks. However, if you happen to lose a game, you lose points based on the ranking of your deck. So, if I use an ai1 deck, I'd only lose 1 point per loss. This was made so people who use wimpy decks don't lose as many points. However, they are also less likely to win than an ai5 person.
These are not biased, IMO. I'm not sure I completely understand why you think it is. I mean, yeah, a person using a lower deck rating would get less points lost per game, but they'd also be less likely to win. As opposed to an ai5 deck user, who would be more likely to win, but when s/he loses, it would hit his/her score harder.