Can you choose the 'type' of advantage? Like "Increased Magery" auto selects 1.5x for me, instead of being able to choose 3.0x (as many people mention). Am I just foolishly missing something?

Yes. Selecting an advantages with multiple variations (such as Increased Magery or Immunity) should change the advantages menu to a list of variations you can choose. It should be fairly hard to miss, so I'm guessing something's wrong with your game, but I'm afraid I haven't the faintest idea what. Does this problem exist with other advantages, or just Increased Magery? What about disadvantages?