In many cases, especially in cost-sensitive designs, you won't want to provide any additional functionality beyond that absolutely required for the project at hand. But since the project is usually a brand new design, you'll need to ensure that the hardware actually works per se and then actually works with the software.
We recommend that you install some form of easy-to-get-at hardware debugging port, so that the software can output diagnostics as it's booting. Generally, something as simple as a latched output that can drive a single LED is sufficient, but an 8- or 16-bit port that drives a number of 7-segment LEDs would be even better. Best of all is a simple serial port, because more meaningful diagnostics can be written by the software and easily captured.
This debug port can be left off for final assembly or a slightly modified "final" version of the board can be created. The cost savings in terms of software development time generally pay for the hardware modifications many times over.