I see two huge differences: overlays and loan program knowledge. There are also differences in cost (big box costs more).
My observations: The big box banks (Chase, Wells Fargo, Bank of America etc) have changed their mortgage loan process since the mortgage meltdown. Rather than going through the expense and time to train (and pay) professional loan officers, their application takers on the front end are not familiar with the guidelines at all for the mortgage programs and once the application is taken, they don't know where it is in the system to provide you much in the way of answers.
The very first person that actually knows the banks underwriting criteria (and all the overlays associated with that particular bank) that will see the application is the underwriter. In the meantime you have provided everything the processor has requested, the appraisal has been ordered, the home inspections done. If you have a very obvious limiting factor, say a vehicle payment, that prohibits you from purchasing the property you placed under contract, no one up to this point (not the loan officer nor the processor) has pointed out that the car payment puts you over your max DTI that the bank allows which is lower than what either Fanny, Freddie or FHA allows. The underwriter reviews and sends you a denial. They don't tell you why. They tell you no. This happens very late in the process, commonly a week before "closing". All of this could have been avoided if the MLO told you at the time of the app. Takes about 30 seconds to calculate DTI's. But the bank prohibits the MLO from disclosing any information that is helpful to you. They want every application to go through the entire process. It wastes your time, money and effort. Note: for a long time Chase reduced (to almost nothing) originating FHA loans but didn't tell any applicants. Chase isn't the only one - but an example.
If you go (online, on the phone, in person) to a lender that only originates mortgages (instead of also handling deposits and vehicle loans), the MLO will know, or should know, the guidelines so you are applying for the right program. If you have a limiting factor, you know right up front at the time of the application what the limiting factor is and how to deal with it. In the case of the expensive vehicle payment, the applicant can get rid of the payment, increase the income or find another property for which s/he qualifies with the payment. Saves everyone time, trouble and money. Most of all the buyer is not making application for a property s/he can't buy and saving frustration and embarrassment. The process is very streamlined. If you use a mortgage banker - they originate, underwrite and fund the loan. The mortgage is sold sometime after closing, but that happens anyway. This is by far the best way to apply for a mortgage IMO. There are many excellent mortgage bankers across the country. Many are also mortgage brokers so they can broker out the loan if they don't have a particular program to meet your specific needs. BTW, quite a few of these lenders don't have overlays which is a huge help (IMO) to the buyer/borrower. Some of these lenders are small banks, community banks or small regional lenders (eg: a lender in two counties only). Some of these are large mortgage lenders in every state (think Guaranteed Rate for example). These lenders have professional MLO's at the front end that are knowledgeable. Their costs are lower IME, both rates and fees. Communication is usually great.
Many, not all, Credit Unions are underwritten by a third party. I'm not a fan of that because the process is bogged down and miscommunication is high. I love Credit Unions for vehicle loans and almost everything else, but not mortgages. Even the big guys (USAA and NavyFed) are very slow and uncommunicative when it comes to a mortgage application.
The next category is what I think of as telemarketer mortgage apps. This would be the Quicken/Rocket Mortgage type issuer. The front end is a telemarketer. They have zero mortgage knowledge and a high degree of denied loans because their front end doesn't have enough knowledge of the guidelines to help the buyer/applicant make application for the right mortgage loan. In my area, if you supply a "pre-approval" from QL, the listing office/agent is unlikely to take your offer seriously. (Same with WF). So who you have as a mortgage lender makes a huge difference.
I wouldn't use a real estate agent to originate a loan.
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WOW. Thanks very much for the perspective. I just advised the intermediary to notify the lende about the existence of a modular frame construction, 2nd unit on a rural parcel although I indicated that the loan officer might not understand the distiinction between modular and manufactured-on-permanent-foundation. Last week a loan officer bought into my premise that two adjoining lots, one with a SFR and another with a 3-plex, can be appraised as a legal 4-plex without a HC, and ordered the assignment as a 4-plex based upon the hypothetical assemblage . . . although the report was kicked out of undrewriting and a new assignment was ordered of a SFR and a 3-plex, which I advised the lender was necessary in the beginning. So I made additional easy money but didn't understand [til this moment] how that was possible. So thanks very much for taking the time to educate a peer . . .