They could leave Red, but I like the suggestions of Giovanni, or Crystal, or a double battle (though in all honesty, I think I'd rather take the two on alone than with a partner). Maybe even different trainers at different times. Just something unexpected would be cool.
As for Jasmine, it could go either way on whether she's coming or going when you face her (if you face her, though I'm willing to bet on it. It could be like when Wallace was champion, I suppose, where you just face her later, but I doubt it). The Gyarados thing indicates you're done with a good deal of Johto by the time DPPt starts, and that's the way I'd prefer it, but it's entirely possible that the thing had been there for awhile before you face it, and that it's in Sinnoh where Jasmine learns of Steel Pokemon. (I highly doubt Ampharos contracted anything from Sinnoh, though - why would she take it with her if it had a duty in the Lighthouse?)
Personally, though, it seems kinda weird that she'd probably have only just returned with her spiffy new Pokemon just before you show up, which it would probably have to be in order to sync up right.
Perhaps they could smooth it over by suggesting that she indeed discovered Steel types there, and when you beat her she suggests that she'll go back for awhile to train and learn more about Steel (that trip resulting in her meeting with the player in DPPt)? Perhaps that's even an in for them to give a new substitute gym leader if you get to challenge the gyms again (her being in Sinnoh), while still including her in the game.
I don't think that's what'll happen, but it's about the only way the timeline makes sense to me. I think I'll look for my copy of Crystal to look again at the relevant part.
The reference I really want is the Silver/Giovanni thing. It seems ludicrous not to do anything with it. :/
