If you are still serious about this, I'd be willing to help you with designing storylines. Also, I can do some scripting as well. Instead of making those 3 be the last Magikarps, maybe you should put in a event called the Society of the Ancient. A group that are trying to forcibly return Magikarp to the world except with a frightening increase in their power. Since you have a Magikarp, the try recruiting you and you have to beat 10 of them, for a grand total of 30 Magikarp (at most) and 30 Gyarados (at most), in a sequence of battles with only Magikarp and if you lose, you have to start the event from the begining. Put it in the begining and your Magikarp will then be close to a Gyarados, and nobody would ditch it.
It's a thought.^ But I mean I have millions. I've already thought of an entire game within the 10 minutes I've seen this thread. I'm just a tad lazy to do ALL of the work myself.
Also, is it cool if I borrow the general idea of Magikarp being basis for the plot for one of my game ideas? I have a couple hundred variations I want to try. Yes. I know. That is a lot of Magikarp.