Changing major parts of the game, like removing the red Gyrados, nixing members of the E4, and removing areas altogether make the game more of a redo or a whole new game. Improving or make slight changes in things would be acceptable. Since the time capsule was used as a means to trade Pokemon between RBY and GSC, it could easily be like a Pal Park option, except without having to walk around and catch the Pokemon, you can just import from the GBA games and deposit them in your PC.
Anyhow, as for the egg you get at the beginning from Mr. Pokemon, I think it WILL remain a Togepi, but if they do introduce irregularities in baby, like the notch-eared Pichu or whatever, then perhaps they could do something with that, since these games are going to 3 years after FR/LG and in the same timeline as DPPt, and eggs would already be known about to a degree. So perhaps the physical irregularities could replace the discovery of eggs. But I'm 90% certain it'll remain a Togepi egg.
As for new additions/addons, instead of making Team Rocket disband completely, expand the story a bit and have the Kanto branch of TR continue their operations. It'd give a little something extra to do there, and perhaps involve the rival (either have him help you, since he turns over a new leaf after beating him on Victory Road more or less), or have something more about Giovanni. That way it could continue the storyline much like it did in FR/LG's Sevii Islands.
