I hate how the plant habitat only holds 500 coins. Especially when the plant dragon has one of the fastest income rates!
No. Two upgrades is all you're getting.
And pairing the high-income dragons with the lowest-capacity habitats (not counting the hybrid and epic dragons) was likely an intentional move on the part of Backflip Studios -- you can theoretically get the most money from a plant habitat, but only if you tap it once every thirty to fifty seconds.
You see the same trade-off of attention time over income in the treat farms as well -- speaking purely cash-to-food the very first treat has a better return than any of the others, but you'll need to give each farm attention every 30 seconds.
You might want to look here for a list of which dragon types and hybrids have the best earning rates, and how to breed them, but generally the bigger the habitat's capacity the slower the native dragon type earns it. (again excluding epic dragons which are really hard to get)
EDIT: A recent update allows you to upgrade "large habitats" to "giant habitats" at the low low price of 25 gems.
Giant habitats can hold more dragons and money than large ones, but even a Giant Metal habitat can still hold much less cash than the smallest epic dragon habitat. (200K versus 500K on the olympus one).
No, one upgrade is all you are going to get. Sorry.
I know some of them are really small like the plant habitat which only contains 500 drahon cash max. Maybe they will upgrade the game so I can. I suggest only have one plant habitat and one plant dragon, plant elements make money quickly so breed it with ice, ground or metal which have large habitats but make cash slower. You'll get the plants speed and the habitat's money.