And, in the systematic event that a law is passed that is grotesque - from the legislative, or in the individual event that a miscarriage of law is applied to an individual case - from the judicial; we need a quick check and balance for either scenario - and the Executive branch is (typically, and on average) the fastest-acting branch of the 3. Lest, one bad-faith branch can reliably depend on its complementary power to be too slow to act (which is happening now, in many ways).
As a result, the executive needs to add tension for either event, and just "Legislative <-> Judicial" having checks against one another in relation to laws, and the judicial proceedings concerning the laws, is not enough.
The threat is lateral, not vertical. The system works by equal tension, not hierarchy.
The "check" to this power itself is also the reach: A pardon does not reach state crimes or civil liability. And the "check" to the person with the power of a federal pardon (the President) is political removal and later criminal charges like bribery - subject to Article 1, Section 3, Clause 7 of the Constitution [1]:
"Judgment in Cases of Impeachment shall not extend further than to removal from Office, and disqualification to hold and enjoy any Office of honor, Trust or Profit under the United States: but the Party convicted shall nevertheless be liable and subject to Indictment, Trial, Judgment and Punishment, according to Law."
1 - https://constitution.congress.gov/browse/article-1/section-3...
I mean, it is a normal thing for a legislature to remove and amend old laws. That's not "a check," but it's a normal part of what it means to be a legislature. You're not just appending new laws, you're maintaining the entire set of laws.
And as for checks, judicial review is the obvious one.