Maybe that guy in Piata IS that scientist. And really, unless they are told to do so, how many veterans of the game are going to talk to a random guy in Piata more than twice? Make it a challenge. Say "Nei CAN be resurrected, but it's up to you to figure out how!"
Of course...you know that somewhere, maybe at PSCave, someone's going to start a thread saying "How do I resurrect Nei in tryphon's hack?", and someone will answer it.
I am personally shocked that no one has come up with a way to alter the code to have Nei stay in your party until now. Even in Numan Revolution, which was a complete makeover (and whoever did it had incredible skills), you had to input a Game Genie code.
OR, and I just thought of this, but I don't know if you can work it in or not...maybe Shir can steal it from a Clone Lab. Make it so she steals a Monomate, like, 99% of the time if she successfully steals, to make it incredibly difficult to get the Genome.
Regarding Nei and guns, I think that would decrease the difficulty level a bit too much. Having Nei and Rudo mowing down robots with Pulse Vulcans would just make it too easy. Having Nei actually INCREASES it late-game if she is mandatory. It's a bit of a trade-off. But that's just my opinion.