There's been a lot of hand wringing since the remakes were announced as to what the Pokedex is going to contain. Since the split Pokedex is practically guaranteed, let's go inside the numbers for a second and see what we can determine. For our purposes, let's assume it's required to go to Kanto.
The baseline for the number of Pokemon in the Johto Pokedex is 130 - that's the number of Pokemon between Chikorita and Celebi, plus any Pokemon you need to get the Pokemon through evolving or breeding. There are certain families that are going to appear because they always do - the Red Gyarados means Magikarp and Gyarados are going to have to appear as a story event and the families that always appear will probably continue to. So yes, you get to be sick of Tentacool all over again.
But that brings us to 147, and Diamond/Pearl caught no end of flak for having only 150 in its regional dex. Certain Pokemon have counterparts, though - the Oddish line has the Bellsprout line, Miltank needs Tauros until they create a calf in the 5th gen and they're probably going to need some Pokemonn to balance
out the ones that only appear at specific times or to stock the Bug Catching Contest.
So how do we get a decent number for Johto (somewhere around Platinum's 210)? It's actually pretty simple. Take the New Pokedex from the originals and toss out the Pokemon you had to bring up from the 1st gen games - 9 starters, 5 fossils and five legendaries. Celebi won't be required as an event, so that gets us to 230. I'm sure we can find 20 Pokemon to toss out to bring it down to 210 while still keeping the Gym Leaders well stocked just by looking at older Pokemon that didn't show up until Kanto anyway.
Here's who I'd ditch:
The Rattata family, the Nidorans, the Diglett family, the Ponyta family, the Doduo family, the Grimer family, the Cubone family, Kangaskhan and Mr. Mime.
By tossing out 20 Pokemon that are either redundant or were original Pokemon that didn't show up until Kanto, you get to a clean 210.
But one concern that's been brought up - what to do with the evolutions or baby forms for these Pokemon that came in since? Consider for a moment that there's 20 existing Pokemon that have evolved or formed a babby since the 2nd gen. Are we going to re-create the scene in FR/LG where you literally could not trade in a Pokemon from outside until you got the National Dex, even if it came from another remake? Probably, if they want to recreate the GSC experience as much as possible. So what do we do?
There's actually a clean solution for this, though. There's 5 babies and they require an item to create. It's a lot easier to breed in the post game, so if I was in charge an item I'd put the breeding items post game and simply exclude the babies from the Johtodex. That brings us to 225. You can take 3 out from Magnezone, Leafeon and Glaceon since they have to be in a specific location to evolve. Leave the Dubious Disc in Kanto, since Porygon2 might be as good if not better than PorygonZ (especially if you go by their Twitter feeds) and put the move returner in Kanto for Piloswine's evolution and you have 220.
Of course, if they choose to deny the existence of the other evolutions I can understand too. I just want to rip stuff up with Togekiss in-game.
This is all my own opinions based on past actions in remakes and my limited knowledge of Pokedex design.
Edited 5/21/09: Forgot Tangela/Tangrowth