What are the most significant issues to consider in “rethinking” homeland security intelligence, and why? What resources are available to substantiate the answer?

It's important to understand why and how the Department of Homeland Security was formed in order to consider this question. The United States suffered a terrorist attack on September 11, 2001 with loss of life that was previously unprecedented, and this caused a great deal of fear as well as, in some cases, an increase in xenophobia and prejudice against Muslim Americans, since the attack was perpetrated by radicalized Islamists. In this atmosphere of fear and paranoia, it was understood by many in the government that extreme measures might be met with less resistance than normal, because of the heightened state of concern and the emotional impact of grief, fear and anger that was being felt in the wake of the 9-11 attacks. So the formation of the Department of Homeland Security was not only an attempt to investigate and help prevent terrorist attacks, but also a way of ramping up nationalist sentiment and quelling general acts of resistance against government itself.
The Project for a New American Century (PNAC), formed in 1992, was a hardline neoconservative initiative designed to fight back against increased volatility in Iraq, and to also seek to justify an increased military build-up (after President Clinton approved a fairly pervasive downsizing of the military budget). The underpinnings of this group's ideology became the basis for the formation of the Department of Homeland Security. Under the eye of this new government organization, initiatives involving increased surveillance of civilians would be implemented, as well as increased attempts to ramp up security in public places and ports of travel. Such initiates can in some cases interfere with individual freedoms and privacy, things highly valued within American democracy.
Going forward, the idea of "rethinking" the practices of the Department of Homeland Security is important because, under President Trump, there has been an increase in negative rhetoric designed to characterize political protest as a criminal activity. This means, in effect, that the DHS had been implementing various punitive policies against US citizens for activities connected to political protest, in response to an escalation in this negative rhetoric. This is not to imply that peaceful protest is in itself illegal or inappropriate, but to point out that, in a healthy and functioning democracy, protest is a legitimate mode of expression to call attention to issues that need addressing. Therefore, the DHS and its role in addressing domestic terrorism must remain focused on those individuals and groups that mean to do actual harm to people or property, and not peaceful protestors.
https://www.sourcewatch.org/index.php/Project_for_the_New_American_Century