All I see is a system designed to encourage cookie cutter characters and actively discourage unique, interesting concepts.
I've never seen a need for aptitudes. I see nothing that makes them better than flat costed advances, honestly.
If you get lore skills cheaper than the rest of the players, then lore skills becomes your thing. If everyone gets it for the same price then the assassin can suddenly turn into a super scholar next week. Background choices looses their meaning.
What I think you might be worried about is not enough freedom to choose your aptitude as you like? Any experienced GM with enough lore knowledge should be able to tweak aptitudes on character creation, so their players can get the background they want without breaking the lore. For a new GM it is nice with some rules that tries to guide them along. And as mentioned, hopefully with more background material released the variety of choices will increase.
Edited by Alox