MongoDB Collection Structure Performance

I have a MongoDB database of semi-complex records and my reporting queries are struggling as the collection size increases. I want to make some reporting Views that are optimized for quick searching and aggregating. Here is an sample format:

var record = {
fieldOne:"",
fieldTwo:"",
fieldThree:"", //There is approx 30 fields at this level
ArrayOne:[
    {subItem1:""},
    {subItem2:""} // There are usually about 10-15 items in this array
],
ArrayTwo:[
    {subItem1:""}, //ArrayTwo items reference ArrayOne item ids for ref
    {subItem2:""} // There are usually about 20-30 items in this array
],
ArrayThree:[
    {subItem1:""},// ArrayThree items reference both ArrayOne and ArrayTwo items for ref
    {subItem2:""},// There are usually about 200-300 items in this array
    {subArray:[
        {subItem1:""},
        {subItem2:""} // There are usually about 5 items in this array
    ]} 
]
};

I used to have this data where ArrayTwo was inside ArrayOne items and ArrayThree was inside ArrayTwo items so that referencing a parent was implied, but reporting became a nightmare with multiple nested levels of arrays.

I have a field called 'fieldName' at every level which is a way we target objects in the arrays.

I will often need to aggregate values from any of the 3 arrays across thousands of records in a query.

I see two ways of doing it.

A). Flatten and go Vertically, making a single smaller record in the database for every item in ArrayThree, essentially adding 200 records per single complex record. I tried this and I already have 200K records in 5 days of new data coming in. The benefit to this is that I have fieldNames that I can put indexing on.

B). Flatten Horizontally, making every array flat all within a single collection record. I would use the FieldName located in each array object as the key. This would make a single record with 200-300 fields in it. This would make a lot less records in the collection, but the fields would be dynamic, so adding indexes would not be possible(that I know of).

At this time, I have approx 300K existing records that I would be building this View off of. If I go vertical, that would place 60 Million simple records in the db and if I go Horizontal, it would be 300K records with 200 fields flattened in each with no indexing ability.

What's the right way to approach this?