I've only been playing for about a year and a half, so I'm nowhere near fully expanded. And, I am still using a bunch of basic habitats. I converted one area from nine big dark habitats to 16 small ones, and in another area I did the same with electric habitats. To gain the ability to move things around, I sell off a grand farm, or two. Since I have millions of useless coins, I frequently sell, and later rebuy grand farms, to temporarily free up some elbow room. In this extra space, I would start the smaller habitats and start moving creatures around.
If you have all premium, four creature habitats, this strategy wont help.you. A square of 9 premiums will hold 36 creatures, which is better than the 16 basic habitat square.