There's not many I think are important, and what answers you get will depend entirely on your definition of a "clone".
I don't consider the American black bear to be a clone of anything in the game, for example. It's "bear-shaped", sure, but a clone?
I could say the Asian small-clawed otter as a "clone" of the giant otter, but I don't think it counts either.
The black-and-white ruffed lemur is about as varied as I think is acceptable, and even that has a lot more variation from its base model than I expected.
So for me, a list would basically be;
1. American flamingo.
2. Sumatran tiger.
3. Eurasian brown bear.
4. Steller's sea lion.
5. Humboldt and/or Magellanic penguin.
6. Tufted capuchin.
7. Asiatic lion and/or southern lion.*
8. Green peafowl.
9. Japanese badger.
10. Masai giraffe.
11. Grevy's zebra.
12. Eastern grey kangaroo.
13. Nile crocodile.
*I am aware of the accepted taxonomic status of the lion, however Frontier has chosen to go a step further and choose a genetically significant subpopulation. Of the genetically significant subpopulations of the Northern lion, the Asiatic is perhaps the most significant, given that it exists within a genetic bottleneck. However, the southern lion as a whole subspecies would more broadly encapsulate actual captive lion populations, as these tend to be non-speficic southern lions (i.e. hybrids between the various southern subpopulations).