Scott Watson fits into that category, his recent application for an Exercise of the Prerogative of Mercy is a diabolical black mark against Executive power forming a remedy for the wrongfully convicted. In the first instance the Watson application took an extended period of time, so much so that in the normal course of events if he were a defendant in a Trial the charges could have been dismissed for want of timely prosecution. Then reading the report into the Watson application, including the manner in which it was looked into, arguably shows that it was not viewed in any merciful way whatsoever. Moreover, common practices of Law, such as individual evidence looked at singularly but also collectively was ignored as has been pointed out in other posts and comments regarding Scott Watson on this blog.
So what does Watson, or others in his situation do? I think there is a clear answer. Take rogue decisions or long delays in recommendations to the Court by way of Judicial Review. I think the old saying of Justice delayed is Justice denied needs to be read with the Bill of Rights. It is a fundamental right that a person know the case against them, that charges or any trial be brought in a timely fashion. When a trial is apparently splintered as in the case of Watson time is of the essence to have it adjudicated by the Courts. The Courts are the home of Justice, not a Government Executive administering 'Mercy' by way of long delays, along with what looks like deliberate lacking of careful Judicial oversight.
I've use this quote by Lord Diplock of the Privy Council before: In de Freitas v Benny  (Court of Appeal in Trinidad), Lord Diplock observed that “mercy is not the subject of legal rights [but] begins where legal rights end.”
Equally interesting are the comments by M Travis below:
1. Some material from M. Travis, May 1998 on the RPOM in NZ.
The whole thing is worth reading, however in the excerpt below is what seems to the answer in Pora – no limits apparent on ‘the discretion’ to exercise. And in the final sentence, what now appears to be a ‘prophetic’ observation regarding a current Judicial Review as, hopefully the Courts and The Executive will ensure that ‘Executive Powers’ are consistent with Statute, due process and Natural Justice – all things which must have been included in the original concepts of the Royal Prerogative. Great observation by Lord Diplock included.
‘The prerogative of mercy seems limited only by the discretion of those who have the power to exercise it – the Sovereign, and the Governor-General by way of delegation in the Letters Patent 1983. Fortunately a precedence has been set by the practice of successive Home Secretaries that, in the words of Ivan Hare , “a free pardon should only be granted in cases where it was established that the convicted individual was both technically and morally innocent.” Although only a precedent and in no way binding, this is most compelling and surely to be followed by successive Governor-Generals.
The only major mechanism that has been suggested for controlling the use of this prerogative is the possible threat of judicial review. So far there has not been a successful appeal for review, but there are many arguments on either side of the issue.
In de Freitas v Benny  (Court of Appeal in Trinidad), Lord Diplock observed that “mercy is not the subject of legal rights [but] begins where legal rights end.” Christopher Gelber considered this a ruling that “the exercise of the prerogative of mercy was inherently extra-legal in nature and therefore not justiciable,” as did Lord Roskill in the G.C.H.Q. case  A.C. 374. Furthermore it cannot be denied that the Crown’s ability to pardon displays the necessary characteristics of a true prerogative; yet there are those like Watkins L.J. who reject the test of justiciability “in favour of an examination of the court’s capacity to weigh the competing issues of principle in each case.” Watkins considered the courts to be competent enough to review the prerogative of mercy.
Nonetheless, a judicial review of the prerogative has never been undertaken in a New Zealand court. The closest thing so far was the ‘review via invitation’ in R v Secretary of State for the Home Department, ex parte Benley  2 W.L.R. 101; where the Divisional Court did not order a formal review but “[invited] the Home Secretary to look at the matter again.” Ivan Hare saw this invitation as attempting to “impose narrower parameters on the discretion of the Home Secretary” via the informal mechanism of invitation, but he seems dubious as to its ability in having any real effect. This is because it is beyond the role of the courts to suggest a particular result, and because any purported limitation on the role of the Home Secretary is illegitimate.
The issue is also a live one in Burt v Governor-General  3 NZLR 64, (1987-89) 7 NZAR and  3 NZLR 672, and some very important contributions to the argument are made. In these cases, Mr Burt sought a judicial review of the Governor-General’s refusal to exercise the prerogative of mercy in granting him a free pardon. Although unsuccessful, Cooke P said that:
“It would be inconsistent with the contemporary approach to say that, merely because [the prerogative of mercy] is a pure and strict prerogative power, its exercise or non-exercise must be immune from curial challenge.”
He states that the Courts’ wish to review the refusal to exercise the prerogative is not “absurd, extreme or contrary to principle” as it is at the very least attempting to ensure that fair procedure has been followed. Moreso he adds that the prerogative of mercy is not “an arbitary monarchical right” but “an integral element in the criminal justice system…a constitutional safeguard against mistakes.”
In conclusion, the prerogative is not to be touched by the Courts or judicial review, yet the concept is one that is winning favour amongst the Judges. It is possible that in a few years there will be mechanisms like judicial review to control the use of the prerogative, but it is very unlikely that it should ever become part of a statute.’
Of course David Bain was the first from memory to succeed with a Judicial Review, at least to the point, of the Minister of Justice agreeing with Bain's counsel to accept a new application from Bain for compensation for wrongful imprisonment. This was after a former Minister of Justice, Judith Collins, displayed a less than merciful grasp of even due process as she set out to apparently take a position opposing an independent finding favouring David Bain's innocence, and his 'right' to compensation. M Travis was quite prophetic in 1998 in his suggestion that in a few years from that time that there will likely be judicial review to control the use of the prerogative. Well, it happened in Bain, possibly years later in my opinion than it should have, but happened nevertheless. There seems to be no known reason that Watson should not take this course, Peter Ellis or Alan Hall, apart from lack of funding. But even that may be contestable on review. For example if a case is made out that is strong enough to support review for Watson or others but funding is denied that decision to deny funding should/is be reviewable.
These approaches can be taken now, with public participation by way of open Court rather than closed Executive Council meetings.