Expression $(1)$ is clear enough in my opinion, in the sense that you can read it as "everything I use as an input is between the parentheses."
Expression $(2)$, while cumbersome, is completely unambiguous. There is a degree of redundancy there, but making things unambiguous tends to make the notation more cumbersome -- it's a tradeoff.
However, I second Misha's suggestion of writing
$$\frac{x^2}{2} \arctan(x)$$
Usually whenever I have a function like that in a term -- be it $f(x)$, $\sin(x)$, $\exp(x)$, $\zeta(x)$, who knows -- it feels more natural to put everything that is not like that to the left of the function. That way there is no still ambiguity as to what is and isn't an argument of the function.