It is confusing that explain() does not indicate whether an index filter was applied. Including this information can significantly help the slow-query debugging process.
> db.foo.insert({_id:0, a:1})
SingleWriteResult({
	"writeErrors" : [ ],
	"writeConcernErrors" : [ ],
	"nInserted" : 1,
	"nUpserted" : 0,
	"nUpdated" : 0,
	"nModified" : 0,
	"nRemoved" : 0,
	"upserted" : [ ]
})
> db.foo.runCommand("planCacheSetFilter",{query:{a:1},indexes:[{_id:1}]})
{ "ok" : 1 }
> db.foo.find({a:1}).hint({a:1}).explain()
{
	"cursor" : "BasicCursor", // no indication as to why hinted index is not being used
	"n" : 1,
	"nscannedObjects" : 1,
	"nscanned" : 1,
	"nscannedObjectsAllPlans" : 1,
	"nscannedAllPlans" : 1,
	"scanAndOrder" : false,
	"indexOnly" : false,
	"nYields" : 0,
	"nChunkSkips" : 0,
	"millis" : 0,
	"server" : "Rassi-MacBook-Pro.local:27017"
}
>