What you are saying, is that Pokemon as we know it would cease to exist without these core features.
I believe this to be true; Pokemon fans new and old are attracted to the games because of familiar creatures. Even a Pokemon newbie likely has a favorite creature, or is attracted to the mythos of a creature like Mew. The Internet has done that much!

Going even further with this idea:
I think it's unavoidable fact that when a Pokemon of a new generation is released, its design and skill set will be evaluated against its counter parts from previous generations. A large part of the new creature's identity actually comes from this sort of historical connection.

There may be free dlc but the only dlc I would be happy to pay for would be regions. I love to explore the past regions in 3D but I don't want just the map and gym leaders. I want it so there is objections in those regions (like gold and sliver with kanto). I would be happy to pay €10 per region or €40 for the bundle for all 5 regions.

Who knows how long they have been working on 3D models. possibly even before Black and White came out. Maybe they wanted to use 3D models before but didn't have enough technology.

Wait, there are differences between the models in Poland vs the rest of the world!?!?!

In all seriousness, I would hope Game Freak wouldn't repeat past mistakes. I almost cried when I couldn't bring my original Red Version Charizard to the beautiful Hoenn Region of Ruby Version.

You couldn't do that due to limitations, Serebii explains the reasoning further somewhere on the site. Transferring between Generations hasn't been a problem since the GB to GBA era.

Like @Morphtorok said, Charizard's data is still in the code, just not as an obtainable entry. I remember shoving the GameShark into Pokemon Ruby, only to see a ton of Pokemon I didn't know back then.

Now, I'm starting to fear cartridge space issues...

3DS carts are pretty spacious, a few hundred models won't be a problem.

If anything since they are letting us change our outfits and accesories, I'd think that's something DLC would include.

I'm almost sure it was possible to get every Pokemon without cheating in the R/S/E games. You could trade a lot of Pokemon from Fire Red/Leaf Green, Colosseum, and Gale of Darkness XD. Also you could receive Pokemon from special events (similar to the Gamestop events they have today).

At the time Ruby and Sapphire were released, we had no idea that any of those other games or promotions would come. Before any of these options came around... These pokemon were completely unobtainable.

They coul've simply ditched all the unused pokemon without anyone noticing, but they didn't.

I really doubt they'd exclude pokemon. Storage won't be an issue (they got 600 something pokemon on a downloadable app, they can fit 700 to a cart) and odds are they've had enough time to make the models.

3DS cartridges go up to 8GB, storage is certainly no issue.