I don't know any smarter way to count inversions in a permutation than simply looking at all pairs of elements to see whether they are inverted or not. In principle, I suppose, there could be. But that doesn't matter, because it would be very unusual to have a good reason to want to know that number for a particular permutation. (The sole exception I can think of is solving homework exercises that check whether you have understood the definition).
Counting inversions is mainly good for theoretical purposes: It's a way to argue that whether a permutation is odd or even is well-defined -- that is, that there is no permutation that can be made both as a product of an odd number of transpositions and an even number of transpositions.
It's not a particularly slick method for finding the parity of a permutation, because there are $\frac{n^2-n}2$ possible inversions to check for an $n$-element permutation, and that number grows uncomfortably fast when $n$ is large.
It is much quicker to find the parity of a permutation by writing it out in disjoint cycle form, and then counting how many cycles of even length there are (an even length cycle is an odd permutation, and vice versa). This can be done in time linear in $n$.
Another quick method (but not quite as suited for pencil-and-paper implementations) is to actually create a sequence of transpositions that reverses the permutation you're looking at, by moving one element at a time into its proper place, exchanging it with what is already there. If you maintain a lookup table of where to find which number along the way, this can be done in linear time too. (Just remember that exchanging an element with itself is not a transposition).