Looks like the start of an interesting and somewhat different game - should fit well with the Wii controller. Wonder if you've found a similar program for the PC?
Re your specific requests for suggestions. With the basic movement you've set up, the only way I see to keep the objects from going underground is to move the half cylinder far enough above ground so that even if an object is directly above it and just over 0.5 meters away, it will still be above ground at the end of the "move toward" instruction. This is because both the while condition and the toward direction are only evaluated after the executions of those instructions (- hence the object's movement back and forth through the "scoop" when they get close to it and it isn't moving.)
(As a comment, I really don't see that the objects disappearing detracts from the game - in fact I rather like the effect.)
One effect that I wonder if is intentional is that all of your "move toward" instructions are "as seen by the world" instead of as seen by the object (the default). In particular, since the tetrahedrons do not start out oriented toward the world, they move in a rather different pattern than the spheres and cubes. You said you wanted to "mix things up a bit" and this approach certainly does that

- but it was a bit confusing when I first looked at the game and may also give you a bit of a problem when you get to scoring a "catch".