On the flipside, he could also be in some sort of double battle alongside you for some reason. It would defeat a lot of points made in the R/B/Y, but at least Giovanni would be set in stone within the game. At this point, we don't even know if he's going to be in the game or not.
I just wanted to echo this point from a couple of days ago.
I've been a fan of TR since I crossed Nugget Bridge back in my Blue version and that fellow at the end offered me a post in Team Rocket. Unfortunately, the game says you can't join, but oh was I tempted (and having said that, I just realized how strange a kid I was...). Giovanni has always had a special place in my heart as a result, and I was rather disappointed in the original Gold/Silver that the TR plot fizzled without any information about him.
FR/LG reminded me about the plot point that he vowed to better himself after losing to Red in the Gym Battle, and he disbanded Team Rocket right there as a result and then vanished. This was a good ending for him in Red/Blue (etc), but it would have been nice to see him three years later, reacting to the fact that people are still following his tainted ideals.
Which, I would propose, would be a good use for Kanto in these remakes. Kanto has very little storyline to it in the original Gold/Silver; it was more of an afterthought than a real part of the game, and though it was fun, it was insubstantial. Nice to revisit, out of sheer nostalgia, but overall fairly pointless. The storyline here could potentially be expanded so the Team Rocket branch becomes more militant once the Johto group is defeated, and Giovanni himself stages his appearance and tells his disciples they were misguided. He seems like the kind of guy that would get fed up after three years of people committing acts of injustice under his name when he already disavowed relationship with the group.
It could be little more than a cameo appearance at the climax of a secondary storyline, although I think it would be a nice touch if he came out and allied himself with you in order to diffuse the threat and redeem himself for his past transgressions. (Seriously, Giovanni needs more love; he was such an integral part to the originals, it's a shame to see him just disappear).
I apologize if this was already brought up; I haven't perused the entire thread to look over it.
Also, Silver as Giovanni's son? I would not be opposed, but the mention in FR/LG seems more like a shout-out to the manga than anything to be pursued in later games. But, like I said, it would be a nice plot to pursue. Silver needs backstory. IIRC, he was just a thief who had it out for Team Rocket back in Gold/Silver, so giving him some connection to anything would be most welcome.
Steal Pokemon for Profit! Sell Pokemon for Profit! All pokemon exist, for the glory of Team Rocket. Oh the good old days...