15 miles are a long way to run. soa natural?

Not quite true (see below): It depends what 'is/are' is referring to. In this case 'is' is referring to 15 miles being A thing, or "a long way". "A long way", and "A way" in particular, is singular. "These shoes are hard to run a long way in." is in referring to shoes (plural) being bad, so you use "are".

I think...

I wanted to add something, because I don't think what i said holds up:

15 miles is a quantity of miles. You can have multiple quantities of things: 5 miles, 10 miles, and 15 miles are multiple distances. 250 mL of water is a quantity of water, or a cup of water.

It is still true that is/are depends on what you are referring to. "Is", in your case, is referring to the 15 miles, but 15 miles is a single quantity.