There are several companies that provide an API on top of ACH. I work for one[1]. For high volume ACH (like a payroll company) it's usually cheaper to go through an API provider than it is to go directly through the bank. I'm not exactly sure why. Maybe because we handle technical support? We also have better reporting.
One of the challenges for banks is that there is an oligopoly on the software that runs the bank. There are 4 companies that provide the "core banking" software to most of the banks in the USA. The banks get stuck providing you with whatever services one of these four pieces of software is capable of.
From my experience it's extremely rare even for large companies to directly deal with ODFIs.
Typically there's AT LEAST one intermediary payment processor (like Chase Paymentech) involved in the TX.
The downside to this is merchant has to register with multiple processing entities but things like "send and forget" APIs (so no need to batch things manually) - which makes it easy to combine ACH and CC payment acceptance in the same system, reporting/reconciliation, out of the box UI merchant can use to look up transactions etc etc outweigh that inconvenience.
Our pricing is typically in the range of $.05-$.35 flat fee per transaction depending on various factors. The main one being your monthly transaction volume. We have a monthly minimum of $250.
We never charge basis points but places that do might make more sense for people who have low volume and low dollar amount transactions. I would say a lot of brick and mortar businesses fall into this category.
One of the challenges for banks is that there is an oligopoly on the software that runs the bank. There are 4 companies that provide the "core banking" software to most of the banks in the USA. The banks get stuck providing you with whatever services one of these four pieces of software is capable of.
[1] http://acheck21.com/api/