I would leave the Instructions just as they are. The game description starts by mentioning "thinking outside the box," so I automatically assumed there's something about the controls that I'm not being told.
Yes, the searchlight level caught me out, but when I couldn't see my character, I started to assume the mouse was involved.
I am plagued by a white rectangle under the house. Objects sometimes appear there and I can only find them by moving the mouse until it changes to a hand; I can't see anything under the rectangle.
It's not clear what to do once you reach full evoluton. The chekpoint system is also really frustrating. It'd be nice to have preset checkpoints that you can initialize by walking over them.
The Yo Dawg quest is not worth spending hours in a game-type I don't like. I work in customer service. It is not a game for me. And I do't get tips for dispensing milkshakes at exactly the right second.
I just want to point out that the first upgrade costs 5 points and the second costs 10. If you buy the first, then the second, you pay 15 points. If you wait and only buy the second, you only pay 10 points. Thus, it is cheaper to save your points for larger upgrades.
I love the uniqueness of this game (and all Nerdook games) but feel that the iPhone version could be better presented. Have you considered creating tabs to allow the player to go from the puzzle screen to the revealed clues screen? The puzzle is too small when it's crammed in with everything else on the tiny iPhone/iPod screen.
One problem I've noticed and I've seen many complaints in this board, is the moving character command menu. If you glue that menu to one corner of the screen (not attached to characters as it is now), that shouldn't be an issue any more. I'd also like the enemy movements (ahem... Ogres) to be actual movements instead of, "I'm going to leap from here to all the way.. no, I'll just stay here." and I agree with the people that want a reset for character stats/ upgrades.