I think you mean V3. Danganronpa 3 is the actual anime That said, I always figured that at some point during the run of the show, they would have switched over to using the same Neo World Program used in Danganronpa 2 for all of the seasons. Mainly because some of those executions were kind of ridiculous. And they could do crazier things. Also, deal with real death less
That said, based on V3, the earlier seasons were literally animes When youre in Shuichis lab, he looks at the files (which are files of all the deaths and method used in the other killing games). And the first few sets were apparent drawn. They they start having real pictures in the later files So, theres that