The problem with those higher earning habitats is that they also cost a lot more coins!
Red rocks only cost you 5000 coins, and earn only 2500, but you will have those 5000 earned back in no time! It only has to be filled up with coins two times to get the cost back. And everything after that is all profit.
The water habitats are 60.000, carry 3600 coins, so they will have to be filled up with coins about 17 times. If you earn about 1000 coins an hour, you could potentially make 19.000 a day (as you can't collect while asleep), still takes three days to earn those coins back. Only then you will start making a profit out of them.
Light and pink habitats, seems nice as they can carry 7200/7500 coins. But are 360.000 coins each for the big ones. Let's say you've got them filled with dragons making about 3000 coins an hour. That is about 60.000 a day, that takes about 6 days to start making a profit!
Besides the dragons also take a lot more apples to gain levels, so leveling them is more expensive.
I would say invest in the cheap habitats first.
And I also think it is a good idea to spread out the dragons. This way you spread out the earnings over several habitats, it will take longer for the habitats to be filled up. But this also means not as many coins will be lost, when you are not in time to collect them.
3 dragons in a fire habitat, each earning 500 coins an hour, give 1500 coins an hour, this means in 1 h and 40 minutes the habitat is full, and coins start getting lost. If you always collect within that time it doesn't really matter. But if you spread them out, 3 habitats each 500 coins, you only have to collect every 5 hours. And within ten hours that habitat has paid for itself. You'll make 20.000 coins extra profit a day.
That does not seem a lot, but if you do the same for the other cheap habitats, it starts to add up fast! And buying those more expensive habitats it not a problem, nor is expanding.