OK, I get it. Not mad at you by the way (I have no reason to be, since the hack itself wouldn't exist without you), you have a good point about the Hoenn starters...
Now as for the Cyndaquil event, the evolution probably wouldn't be as much of a problem (I'm sure Typhlosion can smell just as well as Cyndaquil) but you're absolutely right when you mention the possibility that Cyndaquil has been deposited. Here are two ideas for that:
1. The player is the one to notice the kidnapped Cyndaquil, he either hears them or sees a Knox grunt running down an escapee.
2. The player has to pose as a Knox grunt to infiltrate a hidden base on a specific mission to free the Cyndaquil. As part of his cover, he can be required to bring a Cyndaquil with him (he can say he caught a runaway?). There are still the previously mentioned flaws, but if he has to have Cyndaquil with him, he can't deposit it, and you seem to have prevented Cyndaquil from evolving for a time (for which I hate you just a little). But in any case, it doesn't even necessarily have to be a Cyndaquil that the player takes "hostage." Another option would be that the player teams up with a Legendary Pokemon (or someone makes a mock-up of one) and pretends to be taking it to the Boss.
The most awkward part of this event (for me) would be finding a way to change the players OW sprite temporarily to look more like a Knox Grunt...
Anyway, thanks for hearing me out. Again, and I guess I've said this about a million times by now, you've done a great job with this. Keep it up!