What you say is perhaps the way it should be, but not precisely true either. The reality is that the DOJ has an absolutely incredible degree of leeway and discretion in terms of its enforcement agenda and priorities.
This is nothing nefarious, just the inevitable outcome of the confluence of the following factors:
- The sheer number of laws on the books
- The overwhelming number of potential law enforcement actions possible as a result of the above
- The limited resources of the DOJ
- The reasonable expectation that the DOJ exercise judgment in enforcement actions (e.g. murder cases are higher priority than shoplifting cases, which might not even be pursued at all) and not use a totally unbiased but stupid approach like a strictly ordered queue ordered by filing date
Note that the DOJ having discretion is not the same as a single, all-seeing mastermind at the DOJ directing traffic on all possible investigations and enforcement actions. In many cases it is the emergent outcome of policies developed to translate law into rules, discretion exercised by bureaucrats at various points in the process, etc. that ultimately decides the path of a case.
It might also be the result of purely political policy decisions by the members of the executive branch or others with the ability to influence enforcement policy. Many people are only now beginning to understand the extent and magnitude of this factor as you see the absolutely stark contrast between the Obama administration's policies and those of the Trump administration. Policy decisions by the executive branch can decide whether or not you get deported, whether or not states condoning recreational marijuana sales get busted by the FBI/DEA/ATF etc., and how aggressively (if at all) DOJ pursues certain types of potential violations (e.g. ADA & IDEA violations) through very direct and transparent means like executive orders, or more indirectly through methods like withholding funding or authorizations required to staff an enforcement division.
"What the DOJ cares about is irrelevant" might be the way it should work in theory, but not how it works in practice. There was nothing inevitable about the DOJ handling the case the way it did (indeed, nothing inevitable about them handling the case at all--if not outright de-prioritizing the case, many of these issues are resolved differently based on the highly variable inclination and ability of DOJ personnel to convince parties to go through ADR/mediation rather than issuing an order or proceeding through litigation). To be clear, I'm not necessarily saying the DOJ mishandled the issue or made misjudgments, I'm just pointing out that they did in fact exercise judgment (it's just the way these things work in practice).