When I first tested
Azendohsaurus (Flynn et al. 2010, Figs. 1,3) the large reptile tree nested it with Trilophosaurus (Fig. 2). Then when the post-crania was verbally described in an abstract (Nesbitt et al. 2013), the large reptile tree nested it with Pamelaria, a protorosaur taxon with a single median naris and a short tail. Ultimately, Azendohsaurus and Pamelaria were an odd fit, only mitigated by the fact that Azendohsaurus is an odd fit no matter where it nests.
Today
Azendohsaurus once again nests with Trilophosaurus, not far from Mesosuchus. The former has lateral nares. The latter has a medial naris. Azendohsaurus also nests not far from Noteosuchus, a taxon that shares with Azendohsaurus a short tail, but the skull is unknown.
Evidently
there is a large and varied grade of sphenodontians of which we are just becoming aware. Some of these, of course, include Priosphenodon and the rhynchosaurs.
There are many differences
between Azendohsaurus and Trilophosaurus (Fig. 2), but there are many more differences with the other 543 taxa in the large reptile tree. The presence of long teeth in Azendohsaurus set apart from all other sphenodontians. The very tall and narrow ascending processes of the premaxilla and maxilla are also oddities best matched in Mesosuchus.

Figure 2. Trilophosaurus has filled in the lateral temporal fenestra, reduced the orbit and increased the upper temporal fenestra, among other differences with Azendohsaurus.
I’m sure the definitive paper
on Azendohsaurus is ‘in press’ somewhere. Let’s see how this all turns out.

Figure 3. DGS applied to the skull of Azendohsaurus. Note the new addition of a lateral naris, not previously noted.
Despite the obvious irony,
it appears that few hypotheses in paleontology are set in stone at present. And I’m always happy to set the record straight whenever I can.
References
Dutuit J-M 1972. Découverte d’un Dinosaure ornithischien dans le Trias supérieur de l’Atlas occidental marocain. Comptes Rendus de l’Académie des Sciences à Paris, Série D 275:2841-2844.
Flynn JJ, Nesbitt, SJ, Parrish JM, Ranivoharimanana L and Wyss AR 2010. A new species of Azendohsaurus (Diapsida: Archosauromorpha) from the Triassic Isalo Group of southwestern Madagascar: cranium and mandible”. Palaeontology 53 (3): 669–688. doi:10.1111/j.1475-4983.2010.00954.x
Nesbitt, S, Flynn J, Ranivohrimanina L, Pritchard A and Wyss A 2013. Relationships among the bizarre: the anatomy of Azendohsaurus madagaskarensis and its implications for resolving early archosauromroph phylogeny. Journal of Vertebrate Paleontology abstracts 2013.