I've recently been reevaluating gen 3. I always liked it, but it's gone up in my estimation now.
RSE were very ambitious, given how much was added compared to the previous generation, and all of its features intertwined in a way to make the world feel that much more cohesive.
Just to list a few things that were added or changed from gen 2:
- double battles
- secret bases
- natures
- berries
- contests
- abilities
- mixing records
- regi sidequest
- battle frontier
- reworking how stats work under the bonnet (unfortunately making it incompatible with previous gens)
Berries replace apricorns to an extent, but what I like about berries is the flavour text associated with them - as in literally the flavours. They could have just had a bunch of berries and had a chart showing what colour they were and thus what kind of pokeblock they would produce, but instead they had different flavours and those flavours relate to pokeblock colours. It's a small detail but it adds to the believability of the world because the flavours have a function in gameplay but it's quite minor. It lets you imagine that they're used as ingredients in food in different ways in-universe.
I've said before that I wish contests had stuck around past gen 4 and been developed to the extent battling has been. Out of all of the side-games (contests, pokethlon, pokestar studios, etc.) contests were the most developed and the most fun in my opinion, which is funny considering they were the first. It makes sense that there would be pokemon contests in-universe and the mechanics surrounding it weren't exclusive to contests; berries make pokeblocks but they're also held items and safari zone bait, the moves you use in a contest are the same moves you use in battle but you have to optimise differently.
Natures were a good addition to the battle system in a way that makes it more complex and makes each pokemon species more unique. They
also introduced some abilities that had out-of-battle effects, again expanding the scope of the world beyond battling. Breeders probably use magma armour, for example.
Secret bases were a fun little diversion. There's not much to say about them by themselves, but they contributed to the sense of exploration in the game. Going caving or diving and finding a secluded spot with a spot in the wall is a fun experience. They also worked well with mixing records. This was before we had internet connectivity but they wanted to expand beyond just connecting with people 1:1. Mixing records was like a built-in form of virality. You'd not only mix records with your friend but anyone who your friend had mixed records with, I think that's a genius soluton. It's something that can't really be replicated these days
because of the internet connectivity. There's something magical about connecting with people locally and forming a web of connections. It's something that Nintendo did again with streetpass on the 3DS but hasn't been replicated since.
Actually I'm making an assumption here, I have no idea whether mixing records is transitive (i.e. if person A mixes records with person B, who mixes records with person C, then person A's data might end up in person C's game), if it wasn't, then it was a wasted opporunity.
Battle frontier didn't last long before they axed it so I only really have the gen 4 one to compare it to, but I think I prefer the gen 3 one. A lot of the facilities were more experimental so while the battle pike was just pure RNG and I still don't really understand how the battle palace is supposed to work, I appreciate their attempts to make interesting twists on battling mechanics. The battle pyramid I expecially like because they made a roguelike minigame using pokemon mechanics! Most of the facilities have an element of risk/reward to them that isn't present in normal battling; in the factory you can choose to swap a pokemon to gain an advantage in your next fight but it might put you at a disadvantage later, the pyramid has you choose whether you want to battle more to reveal more of the screen at the cost of your pokemon's hp/pp and the more you explore the more likely you are to encounter wild pokemon that hurt you but you also get to find items that you can save for later.
All in all the gen 3 games just had a lot of effort put into them. A level of effort which I don't think is possible for modern pokemon games due to time constraints put upon them by management.