Excellent news, everyone! I managed to get a fully functional Regional Pokédex running on the 649 Patch. That's another thing that RSE had over FR gone! :D I tested everything I could think of, including seeing and catching a wild Pokémon, the checking of the Pokédex (for counting species caught, obviously).
However, should you download the patch, you will find the "regional" dex is still the Kanto Dex. What gives?
Well, I simply pointed the 2 tables (national and regional) to exactly the same table, in 2 different places. The table at 0x726120 is the National Dex Table. I wouldn't advise modifying this table, since it will also screw up the regional dex! The regional dex table is MUCH later in the ROM (I only just got it working after all! ). It's at 0x762BB4.
How it works (if you're not using PGE - if that's the case, you're mental! ), is that each Pokémon has a "slot" on the table. Bulbasaur being slot 0 etc. To assign a regional dex number to a Pokémon, you go to its slot on the table, and change it to where in your Pokédex you want it to appear. Couldn't be more simple than that, could it!? What I actually mean by this is, say, we wanted to assign Pikachu slot 50. For whatever reason. We would navigate to slot 25 (because that is Pikachu's in game index number) and change the value held there to 32 00. Understand? Bear in mind that it operates by INDEX number, not by National Dex Number, so you will need to cross reference the values with the stdpoke.rbh file I have uploaded as well.
To define the length of your actual Pokédex, simply modify the value stored at 0x763178. You have to set it to the length of your Pokédex - 1. That is, you would set the value to be FA 00 00 00 if you wanted 251 Pokémon, or 96 00 00 00 if you wanted 151.
One last note, I did NOT make the dex in such a way that it could support a slot 0, although it would be easy to add. So no Victini in slot 0 for you Unova remakers. Sorry!
The only thing it doesn't correctly do yet, is count your seen/caught totals correctly. I'll get that fixed in a few hours when I find the time.