The new query system does not implement the optimization described in SERVER-5063. We should reimplement it for the new query system.
For example, if you have an $in query and you specify a limit, then the limit can be applied to each element of the $in. Let's say that you have index {a: 1, b: 1}. The query
db.collection.find({a: {$in: [1, 2]}}).sort({b: 1}).limit(5)
can be executed by limiting the results from a==1 to 5 and the results from a==2 to 5, sorting on "b" with a merge sort, then reapplying a limit of 5. Currently this query is executed with a mergeSort, but the limits are not applied to the children of the mergeSort.