The main issue is it being a JSON document store, and our application being designed around that and using the very specific MongoDB queries that involves.
Any wrapper would likely be worse than just keeping MongoDB.
We have the exact same issues with Mongo-specific queries. Even worse, our indexing regime (because we store relational data in Mongo) demands that we stick with Mongo 1.8, so all the comparative goodness of 2.x is lost.
And just this week, it was determined that there won't be any migration from Mongo to something-SQL in the near future, because it'd be too risky to attempt to translate a schema that's half foreign keys, half embedded JSON.
Any wrapper would likely be worse than just keeping MongoDB.