why would being in 3D make it better?
It would add another dimension to it, of course!
With physics-based gameplay, a third dimension can actually be a pretty big deal. Now we can have things spiralling down funnels, winding pathways that really are windey, err, etc.
I pondered this once with a sort of dominos focus, then I realized that I already had an idea to pursue (and I somehow turned my spin on the design into pure garbage) so I forgot about it.
Done right, it could be very interesting. It needs some pretty clever design to be fun, though; designing real masterpieces is a rather slow and meticulous process although you
want the player making ridiculously convoluted machines! It has to be meticulous, but not be a battle against the interface. Any complexity has to be entirely within the game world, or it will be horribly irritating thanks to the amount of time spent with the builder interface.
Something tells me good sound engineering (and lots of sounds) would breathe life into such a game.
If you haven't seen Electroplankton, I suggest you take a look at it; that kind of interactive (adaptive) music / dynamic sound could be quite a nice background thing to keep it interesting.
A tetris style gameplay may be interesting, where different components get randomly handed over one by one, and the player can only use a certain number of them. That way he can't just drop the components he doesn't want into a corner until the one he wants appears; he has to use what is given to him! It would make for the sort of crazy machines we want while also preventing people from devising exploits.
That would also help, perhaps, to get the different levels a bit more malleable. Instead of having a specific set of objects given out for each level, you could have a bigger library of objects available to the player, and perhaps objects that are forbidden from appearing in the level (and objects that appear more often).
I find it a shame (though really just lame) when a game's salesmanship blurb says "You can build your own [blah]!", while really all you can do is either: Paint an existing object, create your own ridiculously simple inanimate and useless object, or point and click to create a rigidly defined object as though you are building it yourself while you are really just dragging objects onto certain places (oh boy, exciting!).
That's why Spore is so exciting, is because it breaks from that mould. For something like this, you would want to break from that mould as well.