Why does Magneto seem to care more about Quicksilver than Polaris?

The game came out in 2005 and her being his daughter was resurrected in the comics in 2002/2003.

So, my guess is the game makers were old time fans that didn't accept the change yet.

TL;DR : While it is true that Magneto's relationship with his children has always been very complicated, he has always seen Pietro as the one who would carry on his legacy.

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Even before he revealed the relationship to the Twins, Magneto was adamant that the two - especially Quicksilver - believe in his cause of mutant superiority and work to further that cause. Magneto was devastated when the pair left his Brotherhood of Evil Mutants, going so far as to kidnap them and make them return by force (Avengers Vol.1 #48 way back in 1968):

In fact, it was largely because of his children that Magneto turned over a new leaf and attempted to achieve his goals in a peaceful manner. It was his hope that if he could strengthen the relationship between himself and Pietro, thus convincing the boy to follow in his footsteps. In fact, no matter how rocky their relationship at the time, Magneto has used every opportunity as a chance to mold Pietro in his own image:

Magneto has never been particularly close to Polaris, which is ironic given that she is the one child out of three who accepts their relationship.

They're both magnetic personalities. Clearly they repel each other. Honestly, he raised the twins. Polaris is new. Not the same bond.