The correct answers are: I'll take the chocolate cupcake, and also that strawberry one. These vanilla cupcakes look good, but I prefer the chocolate ones.

We use one to replace a singular countable noun (like cupcake) to avoid repeating it.

We use ones to replace a plural countable noun (like cupcakes).

"A stale ones" is incorrect because "a" is singular but "ones" is plural. "Three big one" is incorrect because "three" is plural but "one" is singular.