Each bank sets their fees to what they feel is competitive for the types of loans they are making to the market they are serving.
Not always, but often it has to do with service as better service usually means more fees, so determining which bank to go with should take into consideration the terms, fees & service being provided - collectively called the "value". Perhaps one bank charges lower fees but will not explain things as thoroughly or doesn't do as much of the work that needs to be done as you would like, perhaps one bank charges a lot of extra fees for services and assistance you can do without, etc. You'll have to thoroughly examine your own needs as well as how each bank can meet those needs and under what terms. Part of the answer will be analytical, part of the answer will be how you personally feel.... more