They should stick with the current mechanics (EV/IV system) but reintroduce IV and shiny breeding and stuff like that. There should be at LEAST 500 pokemon total including the 386 we currently have. They're linking Emerald to the new ones so that's the gateway between generations. Using that you should also be able to access stuff like Contests and stuff... They should definatly bring back day/night and the days of the week having something similar to the pokegear, that was by far the best aspect to G/S/C. They should also release a brand new set of 50 TM's but allow the Advance TM's to be traded over and labeled as something like "TM 06A" for Toxic. More move tutors and egg moves and stuff are a given as well as brand new moves. These games can pretty much just take the Advance generation and build more on top of it, leaving everything on the bottom still there for everyone who likes it.
For the full 500/whatever pokedex there should be some Ru/Sa/E and FR/LG ONLY guys so they still have the incentive for people to buy those and a bonus for those who allready have it.
I think they should bring back Johto for a little honestly. That was my favorite region of any game. Hoenn is plugged right into it with Emerald so that isn't an issue and Kanto isn't that far and we've had it in every single generation so I don't think anyone would miss that for a little especially when they can send thier guys right over to emerald and then to Diamond/Pearl. They could really make these games have the best of every world and make it work. I mean hell, having ONLY new guys in the main game would be real cool too, then you just trade all the others over or something. That may seem like the "Two steps forward, one step backwards" that I felt about Ru/Sa for a while but you CAN just send all the others right over so that wouldn't be a real problem I don't think.