Why some people improve faster than others? ?

you say they started the cross country together and finished together.  i think they ran together side-by-side.

Because people's bodies are different, people's effort is different, people using the same training plan don't train exactly the same (they workout differently, eat differently, recover differently), and people's abilities are different. It would actually be odd if everyone progressed/improved at the same pace.

There are different reasons.

What are the differences between the two people in your example?

It may be one of your athletes was more active before the first practice. One might have been running, playing soccer, or swimming while the other was reading, taking extra classes, or designing things while sitting at a desk.

Are they built the same? Maybe one has a better build for running. Even when two people have body types suitable for running, it might not be the same type of running. One may be built to be a sprinter, while another may be built to be best at 10 kilometers.

What about motivation? Is one driven to workout more or harder than the other?

Do they have the same health history? Was one seriously ill, while the other avoided serious illness? Was one seriously ill more recently than the other?

Do they have different living conditions? Does one live in building with good air quality, while the other lives in a "sick house"? Does one live in the city, while the other lives in the country? Is one poor,  while the other middle class? 

Does one have a healthful, well balanced diet, while the other eats a lot of junk food?

What are their genetic differences? 

There are several factors that influence our athletic potential. Each factor has a different weight. The pluses and minuses interact. Pluses can work together to make a better athlete. Minuses can work together to impair athletic potential. Pluses and minuses can interact, offsetting each other in different ways. Gifted athletes have stronger pluses and weaker minuses. 

Edit: 

Genetics is a big factor. Genetically gifted athletes can work out harder, longer, and more often before they suffer the consequences of overdoing it (overtraining syndrome or burnout). This allow them to develop their ability faster and to a higher level.

Comment: A runner at our high school mentioned his morning workout. Another runner, surprised, said "You work out twice a day?  You're nuts!" Another runner said "He's not nuts. He's the state champ." 

It's almost as if every person had their own unique DNA and physical attributes.