frankthedm: You're talking about centering a spell on an intersection. I was talking about centering it on the middle of a space. I'm not sure if 3.5 RAW required centering on an intersection, but I'd argue the same principle for centering on a space for that, too. But in any case, I think you'd agree that a sphere allows for some placement that does not include a full 20' radius.
Styracosaurus: I just don't see this as manipulative, only using your power to the best of your abilities. And I still think it's rather germane to air-based or water-based combat (altho the DMG never actually answers this question in either of those descriptions). I would think being able to avoid small-sized creatures and only hit medium-sized creatures is more along the lines of being "manipulative," but prone, unconscious creatures vs. standing, medium creatures? There's got to be over 1/2 a "square" difference between the two. Why is it manipulative to shoot a power 1/2 a square higher?
Leatherhead: I think bursts are certainly cubes - they do say 1 square in every direction from the origin. But why are blasts squares? Couldn't they be cubes as well? I have always thought of blasts like cones, but then again that's probably because the first blast I read about was burning hands...
So folks don't seem to have a problem with aiming high to hit larger creatures and missing medium creatures: so why can you not apply that exact principle to 1/2 a square up instead of a full square up? Not that realism has really anything to do with this point, but I would think a wizard using thunderwave could easily move his origin point 3' up or down instead of just 5', especially since he can choose any point along a 5' line to originate a blast.
In fact, I may have just proved my point. If you look at the two blast examples in the PHB on page 272, the lower one starts in the corner of one space, and the other effectively has a point of origin that is in the center of the wizards north (top) square. The center is effectively 1/2 a square over with respect to how that mini is situated. I think this shows you can move 1/2 a square up or down, as well - just imagine the lower blast example with an origin point halfway along the wizard's south (lower) side.
The main question left is whether or not a blast is a cube or a square. (I still lean toward cube, like area effects.)