I might be a bit biased in the "dumping Pokémon part", since I'm partial to all Hoenn Pokémon, so bear with me
Anyway, adding new pre-evos will be much easier with the adding extra incenses tutorial some dude called Jambo51 made. Kudos to him btw, he's basically doing everything that lazy bums like me wish. Keep in mind that this invariably means that we must change evolution methods for Happiny, Mantyke,etc., because their methods involve unnecessary complications. That is, unless we can add custom routines into the mix. Lol we may have to dump quite a few since Gen IV introduced the largest number of cross-evolutions. That is:
Magnezone
Lickylicky
Rhyperior
Happiny
Tangrowth
Mime Jr.
Electivire
Magmortar
Leafeon
Glaceon
!Sylveon
Porygon-Z
Togekiss
Bonsly
Ambipom
Yanmega
Honchcrow
Mismagius
Gliscor
Weavile
Mamoswine
Mantyke
Gallade
Probopass
Budew -> (Roselia) -> Roserade
Dusknoir
Chingling
Froslass
I basically singled out the Gen IV evolutions from Bulbapedia (excluding Sylveon which isn't exactly accessible right now but meh).
Sooo yeah first things first: Which all do you want?
Anyway I would suggest kicking dust off some Johto Pokémon, since they aren't that many (100) and most of them form the lower rungs of Pokémon (exeptions being legys, Tyranitar etc.) sooooo yeah, they give some free space. Additionally, you can take down some from Hoenn if you feel like however I liked all of them so I'm a bit partial XD.
...
Now that Gen II Pokémon have decreased considerably, night schedules wont be hard for them either. Basically check if it's worth adding on the night, if no then put it after Elite Four. We're expanding the ROM considerably so extra maps wouldn't be a bother, will they?
Soo the next thing we do is THE BIG DECISION.
What is THE BIG DECISION? Whether to add a regional dex or not. I recommend adding one but Pokédexes are glitched up anyway and it will be hard to stuff in 235 Pokémon post-game LOL.
Unless you want to change encounters in old maps after the Elite Four, which will solve almost all the problems.
Alright that way these Pokémon are handled XD
But now if you're making a regional dex then start listing the Pokémon included in it!