I am studying set theory and have recently encountered the concept of ordinals. The way I understand them, we are trying to classify all well ordered sets (which have desirable inductive properties) into equivalence classes w.r.t. a relation that preserves the order structure, and have a canonical representative for each equivalence classes, but since these turn out to be proper classes and not sets, we call them order types.
And it turns out that if we take the von Neumann ordinals $\left(\left\{ \emptyset,\left\{ \emptyset\right\} ,\left\{ \emptyset,\left\{ \emptyset\right\} \right\} ,\ldots,\omega,\omega\cup\left\{ \omega\right\} ,\ldots\right\} \right)$ then we can prove that any well ordered set is isomorphic to exactly one of these, called its order type.
So my question is what's the motivation for the further abstraction of defining an ordinal as a transitive set which is well ordered w.r.t. $\in $ ? Can't we simply use the fact that the von Neumann ordinals possess these properties? Is there any context where we use ordinals that aren't the von Neumann ordinals? Or is my understanding as presented above somehow flawed?
Your misunderstanding is that you think "ordinals" and "von Neumann ordinals" means different things, such that only some of the ordinals in set theory would be von Neumann ordinals.
Since there is really no such distinction in a formal development of set theory, you become confused.
In other words, the sets you're thinking of when you write $$\emptyset,\{\emptyset\},\left\{ \emptyset,\left\{ \emptyset\right\} \right\} ,\ldots,\omega, \omega \cup \left\{ \omega\right\} ,\ldots$$ are exactly the same sets as the transitive sets that are well-ordered by $\in$.
If we want to be a bit more abstract, we could say that an "ordinal number" means "whatever it is that two well-ordered sets have in common when they are order isomorphic". That would be similar to saying that a "natural number" is whatever two finite sets have in common when they have equally many elements.
This is conceptually simple, but not technically convenient. If we want ordinal numbers to be set-theoretic objects (such that we can make them elements of sets, etc), then we need to specify a particular set to represent each of them within set theory.
Von Neumann proposed to represent each isomorphism class of well-orders by the transitive set that is ordered in this particular way by $\in$. This representation is what is known as the "von Neumann ordinals". It's not a particular selection of ordinals; it's a representation that works for all of them.
The von Neumann representation works so well that it has become pretty much universal in set theory.
The reason why we don't just define them as "$\emptyset,\{\emptyset\},\left\{ \emptyset,\left\{ \emptyset\right\} \right\} ,\ldots,\omega, \omega \cup \left\{ \omega\right\} ,\ldots$" is that for rigorous proofs about them we need a definition that doesn't depend on the reader figuring out for himself exactly what is implied by the suggestive notation "$\ldots$" that appears in it.