After a quick read up of their lore, there’s no doubt (for me at least) lore-wise Thorek Ironbrow should be chosen. He’s got a better story and better life goal in the lore. No offence to Malakai but Thorek is also a lot more important to the dwarves and the world as a whole. He’s a Runelord and leader of a dwarf stronghold, Malakai’s only real claim to fame is being a companion of gotrek & Felix, other than that the highest position of importance he got was teacher at the Nuln gunnery school.
HOWEVER, with that being said, the dwarves already have runelords available as lords for their faction. Malakai would open the door for CA to include Master Engineers as a playable dwarf lord. So while Thorek is the better choice lorewise, Malakai is the better choice for the variety of the game out of those two options. There are better Master Engineer Dwarf lore options though besides Malakai.
And of course, this is just my opinion.