Regarding changes to the rules/mechanics, I stick to the official ones. With a few exceptions, I try to make them as modern as possible. So there are abilities, natures, Physical/Special split, 80 BP Leech Life, etc; but no increased level cap, no custom types, no invented damage formulas. Some exceptions: I'm not implementing the 510 total EV cap, because I find EV training tedious and it isn't fun to know that the Pokémon you start with will have sub-standard EV distributions since you battle random NPCs and wild Pokémon. Also, I invented an EV-based evolution method for the four trade evolution Pokémon (Kadabra, Haunter, Graveler, Machoke), but that's minor.
As for plot, setting, and characters: again, they're mostly official. The new maps are either from other games (Viridian Forest, Pewter Museum, Cliff Cave), natural additions (Cinnabar Volcano, Cerulean Cape), inspired by Pokéwalker routes (Yellow Forest, Quiet Cave), or tie-ins to the Pokémon Christmas continuity (Ecruteak Shrine, Shamouti Island). So, no custom cities or Gyms, no completely made-up characters, no drastic changes to old maps just for the sake of change.
The original maps like the Pokéwalker routes and Shamouti locations will be almost entirely optional sidequests. I'm trying to balance staying true to the original Crystal version, along with making the new areas not seem pointless. So they'll have unique features and events, but you can beat the game while skipping them.
Can't provide a reliable ETA, but
this is everything that's left to add. I want to get all those save-breaking features done now so that people don't have to keep restarting their playthroughs with each update.