db.tablebusiness.find({ \"LongitudeLatitude\" : { \"$nearSphere\" : [106.772835, -6.186753], \"$maxDistance\" : 0.053980478460939611 }, \"Prominent\" : { \"$gte\" : 15 }
You are comparing apples with oranges. Both queries return different results. $all means that the field value should match all the inputs whereas $in means that the field value should match any one of the values. $all is and, $in is or.
Combined with the $limit - the $all query will need to look at more documents to find the match as compared to in.