I enjoy this idea thoroughly, but I seem to have encountered a bug in the Randomized mode. I'm not sure if you meant to do this, but when you pick your starter, Gary (or Cancer as I have nicknamed him), refers to either Bulbasaur, Charmander, or Squirtle. I'm not sure if you intended for this to happen or not, but I have started the mode four times with the intention of doing a Nuzlocke Run.
There is yet another more pressing problem: When Cancer fuses the other starters together in Nuzlocke, none of those Pokemon were available as starters. I chose a Tentacool from the choice of it, a Geodude, and a Koffing, but suddenly found myself up against a Voltrio (Voltorb + Duodrio) when Cancer challenged me. And before that, he wrecked my Sandshrew with a Krabdeen (Krabby + Goldeen), even though, again, neither Pokemon were offered.
I'm not sure if you intended for that to happen, but it doesn't seem to process correctly if the rival fuses the two remaining pokemon together. I have had no other trouble minus these incidents, and I hope this issue is repaired in the future.
Thank you for your hard work you spend making this game a reality. I wish you best of luck as this process continues.