sort, hint, snapshot, explain(and more in the future) goes inside {$query :

, /* options */ }
for example: {$query :

, $orderby : {y:-1}}

skip, limit and fields are separate attributes.

There is no reason, other then historical I think, that there are two types of options.

Moving all the options inside the query doc will make the query packet more consistent, extensible, easier to code and understand drivers.
It is an easy change in the drivers and won't break the API.