Hmm... to my knowledge there isn't a throwing knives secondary. That's your Inherent power you get for choosing to be a Natural character.
I mean, you have two main attack sets... look at your powertray. One is a certain color, and the other is a different color. (Not the grey powers). What are the other powers?
As for your Travel Power: If I were you, I'd stick with Combat Jumping, then grab Super Jump. It's one of my favorite powers because 1. You don't need to put as many slots in it (only 3 for jump, whereas with Fly you need 6 slots for fly and endurance cost or you'll fall out of the air). 2. It uses far less endurance, and 3. the power you have to get beforehand doesn't suck.
Now, Hover does have its places... for Corruptors and Dominators (basically anything that has ranged attacks), it's fantastic for the defense, +knockback resistance, and the fact that you're practically immune to melee attacks if you're high enough in the air. Since you're a Stalker, Hover really does suck for you. If you truly want Fly, grab Air Superiority. It has a good amount of damage and knocks foes out of the air (and keeps them there for a good time).