The application process is pretty simple.
We were lucky to be one of the first few companies to get registered without any reference or accelerator tie ups. The fee was waived off for us and we got a $15,000 AWS credit as well.
The biggest advantage in my opinion is the SVB account opening and the fee waiver for the first 2 years. If you go directly, most banks will hesitate to let you open a bank account without huge minimum amounts. Plus, you'll need to visit the bank in person.
The draw back is, the legal agreements are given as templates. We need to edit it to suit our requirements. It's recommended that you have a lawyer who helps you with this process.