Giraud's axiomatic characterization of a Grothendieck topos characterizes it as a locally small infinitary pretopos with a small generating set.
If elementary toposes are like sheaves of sets over a site, then abelian categories are like sheaves of modules over a site. Perhaps grothendieck toposes are like abelian categories with some extra conditions.
I am wondering if there is a characterization of categories $C$ which admit a full and faithful functor $F : C \rightarrow \text{Shv}_{R \text{-mod} } (X)$ on a site $X$, which has a left exact left adjoint. (I am aware of the embedding theorem for small abelian categories, but note that this is different.)
Also, I am interested to see whether certain small topoi have an embedding into $\text{Set}$, in analogy with mentioned theorem for small abelian categories.
Best Answer
An abelian category is somewhat like an elementary topos, but there's a better analogy: the Barr exact categories. These are categories with finite limits and quotients of equivalence relations which interact nicely with pullbacks. Every topos is Barr exact, but not conversely-for instance, categories of algebraic structures are Barr exact but very rarely toposes, since they're rarely Cartesian closed. And indeed, Barr proved in his original paper on the subject that a category is abelian if and only if it's additive and (Barr) exact.
Let me next answer your question about embedding small topoi into sets. This is not again not quite the right analogy to make: we should talk instead about small Barr exact categories. And it's unreasonably to expect to embed them nicely in the category of sets, since for instance the terminal object would then be a generator. The closer analogy with Mitchell's theorem would be to ask that a small Barr exact category $\mathcal E$ embed exactly in a category of right $M$-sets for a monoid $M$, being the non-additive analogue of a category of $R$-modules. Unfortunately, this is still not possible: for instance, the terminal object in the category of $M$-sets has no nontrivial subobjects, while in $\mathcal E$ it might.
However, this is essentially the only constraint. In the same paper referenced above Barr exactly embeds every small exact category in the category of presheaves on a category built out of its poset of subterminal objects. The last caveat is that, outside of the abelian world, "exact" must have a new meaning. Specifically, it means "preserving finite limits and coequalizers of equivalence relations." It is an interesting exercise to see that this reduces to the usual definition of exactness for functors between abelian categories.
Regarding your question on a characterization of exact reflective localizations of categories of sheaves of modules, there is a well-known answer to a slight generalization. Let us allow $X$ to be preadditive and consider additive functors. Then such categories $C$ are exactly the Grothendieck abelian categories, that is, the cocomplete abelian categories admitting a generator in which filtered colimits are exact. One direction of this is the famous:
There is no need to consider a topology on $A$ here, as an exact localization of a category of sheaves is certainly an exact localization of a category of presheaves.
For the converse, it is a basic fact that reflective subcategories of cocomplete categories are cocomplete and that the reflection of a generator provides a generator. Finally, if $\mathcal{C'}\to \mathcal{C}$ is an exact localization and filtered colimits commute with finite limits in $\mathcal{C}$, then they do so in $\mathcal{C'}$. Indeed if $A$ is filtered then all the functors $$\mathcal{C'}^A\to \mathcal{C}^A\stackrel{\mathrm{colim}}{\to} \mathcal{C}\to \mathcal{C'}$$ preserve finite limits by assumption, while the composite of the above string is the $A$-colimit functor of $\mathcal{C'}$.