>The patent mentions the ability to aim the pokeball which wasn't in the first 3 Gameboy games.

Sure but I'd say aiming is more or less the natural evolution of "$X in 3D instead of 2D." Obviously Nintendo disagrees and perhaps the patent system disagrees (depending on the outcome of whatever court cases happen), but I disagree with them.

> depending on the outcome of whatever court cases happen

do you not mean the bribery of patent agents?

>Does modern Pokémon start battles by throwing a pokeball to release a monster to begin fighting?

yes

To answer your question, starting with Pokemon Legends Arceus[1], battles take place in the same overworld that you explore in.

You can see an example of this in action at 3:12 in https://www.youtube.com/watch?v=DR7ZooH9Zos

[1]: This also carries over to Pokemon Scarlet/Violet, which is the latest mainline entry and will presumably remain the new standard going forward? Arceus was seen (and received) as more of a paid beta test for the system since the overworld was a bit empty at times

> Does modern Pokémon start battles by throwing a pokeball to release a monster to begin fighting?

In "Let's Go, Pikachu!" and "Let's Go, Eevee!" this was the only way you could catch Pokémon. Just like the way it is in Pokémon Go. (Or was, haven't played in years)