PartyPoker introduced the 3% fee around the time many players were abusing a 1.5% cashback promotion run by Skrill. PokerStars and other sites detected this and stopped running the promotion, but didn't raise fees.
PokerStars also allows players to request higher deposit and withdrawal limits.
PartyPoker & The Recreational Player Model
PartyPoker has had an interesting history of changes and updates, in its transition towards favoring a recreational player model.
Aug 24, 2011 - PartyGaming switched from the dealt rake method to weighted contributed
Apr 1, 2013 - PartyGaming capped effective rakeback at 30%, by removing the top tier of their VIP program, 'Palladium Elite'. Previously the Palladium Elite VIP level had allowed for up to 50% rakeback