After 10 cells in a colony, the colony should start to grow opaque, like the cells from Spore on high graphics. The colony should grow more and more opaque until 100 cells, at which it is completely solid. Since adding another camera dimension is a large leap, the 100-cell mark needs to only make the change after an editor session, and keep it low-profile. After going 3D you can go on land but you need either to place a seed up there, or make lungs (You won't have legs though) How is this seamlessness?
I think I suggested having the camera tilt more when the colony moves the larger it is (angling to see the front of the colony). I also brought up having the background fade into a sandy seafloor texture in the same way.