The brutality of the first execution was what really cemented my opinion of the game. Though I did think the first one was probably the worst, given it probably took a lot longer to die than the others. Well, except the last one, obviously.
Anyway, it's a great game. You have to purposely overlook a few things that cause plot holes, but most are minor enough that it doesn't matter. It would have been better if the original plan for multiple routes was implemented, but hey, that's what DR3 and on is for.
There were things left unexplained but I don't remember any holes.
I don't know about Cyril but the two big ones for me were
they made such a big deal about the number of lights at the morgue which makes sense... until you realise that Mondo was now an empty tub of butter and would not need to be in the morgue. The bodies were left there to be preserved and plastic doesn't degrade that quickly.
I can overlook the Deus Ex Machina of Naegi being saved from the execution at the last second but how the hell did both Kirigiri and Naegi survive that fall? No way a pile of trash would cushion a fall of that height, especially in Kirigiri's case.