Well, the thing is that when you repoint them, you'd have to repoint them to free space so the new table can be expanded. This obviously will take a megaload of space, so a good course of action will be to expand the ROM itself (this also means you'd have to switch to APS from IPS).
After that you may customize the new everythings, and add the data you need to add. Then of course, after doing all this you can put in the stuff onto the game itself. Keep in mind that you'll have to hex edit to add new Pokémon, as A-Map does not support the expanded tables and stuffz.
It's really simple; you just have to:
Repoint the Pokémon data
Repoint the Pokédex data
Repoint the Footprint table
Repoint the Sprites table
Repoint the Palettes table
Repoint the Icon table
Rearrange the National Dex data
Repoint the Cry Table
Repoint the Pokémon Moves and TM/HM compatibility data
Do some other RAM related expansions
Make a new program like AdvanceMap that accepts the new Pokémon Table
Make a new Trainer Editing software that accepts the new Pokémon Table
The last two can be left out if you are brave enough to hex edit all the data.
Jambo51 is working on a 649 Patch, which includes 649 Pokémon, New Moves, Abilities etc. The best bet will be to help him work on it, cause it's too much work for one person.