That’s not quite what I’m saying. With say, 15 males and 15 females, you can create 15 pairings. If you can clone them, you can make 225 pairings. You still have to worry about inbreeding but you can make many more different combinations of the genes you do have and ensure none of the individual genes are lost by not being passed on.

In addition to your point, inbreeding isn't necessarily a problem if you engage in selective breeding. (Sterilizing and euthanizing animals with fatal recessives or health problems) Genetic testing has made this a much more effective solution. With in-vitro testing and implantation you can clear these problems before the animal is even born or implanted.

The problem is that a lack of diversity can lead to issues with adaptation to new environments and pressures. This is what has made a lot of these species endangered in the first place. They are adapted for very specific conditions which are suddenly changing due to habitat destruction. (Deforestation, urbanization, water works, farming)

A typical population has a lot of mutant lines that do okay in the current environment but may be more adapted to different environments. A population of clones will take time to develop these and may not survive long enough to adapt. Also if there is a problem with the current line and you don't catch it fast enough you are hosed.