Open Source firmware like DD-WRT or Tomato has many features equivalent to what stock firmware has, in addition to adding new features to a router. However, some features are lost from the stock firmware when a router is flashed.
These are typically features that are put into the stock firmware by the manufacturers themselves. Things like the Linksys App and the NetGear Genie are examples of what would not be available or compatible on the router after flashing.
Most routers also have a WPS button. By default, the WPS button's functionality is disabled when a router is flashed as it can be vulnerable and a security risk. It can be re-enabled by following this guide but we do not recommend it.