You can theoretically have a higher rate from one lender with lower origination fees and total finance charges may come in lower.  

They often think they're the smartest people in the room and, as such, they should be in charge. 

I can do that through charging points, but since I'm getting it at a lower rate than you could as a consumer, I prefer to mark up the rate while still being lower than most others in the market.

The brother and his son had been living in the house, free of charge, for years, and were gaming the system.

As you know, marketing and price are both very important, and vacancy will significantly impact your income, so you are almost always better off charging a lower price and getting it filled with a good tenant.  

The agents are charged for this service no matter what so it's difficult for the agent to service from a time and financial perspective.

An appraisal fee in advance for an actual appraisal is legitimate, but you can find lenders that don't require appraisals and don't charge appraisal fees.

then theirs charges 1000s in extra fees. 

It is a violation of the HAP contract to charge more rent for voucher recipients than market rate tenants.

You take a deposit per usual and charge them for any damage beyond wear and tear.