Yeah I was thinking along those lines as well, even though the idea originates from the anime. The only problem is that when you, the protagonist, battles it, Zel would have to make it so that it was uncatchable, otherwise it would be hard to explain how lance got the red gyarados that you caught. Or else he could make it so that lance battles the gyarados instead or something, but still lance already gives you clamperl, so it'd be kinda weird for him to give you two pokemon...
Yea that's true. Perhaps he could be the secret santa of pokemon games? Well, in any case, there should be a red Gyrados, that perhaps Lance catches, and he gives you the red scale. Then later, gives you the clamperl. Or, how about replace the clamperl for the bagon? Because, the secret rocket underground is a place that not a lot of people are willing to go for, but if they hear that you get a bagon at the end, then they may become motivated to do so. Just my two cents. =)