3rd Gen Would you say these games were the beginning of when Pokémon plotlines started to get deep?

With Pokémon Ruby and Sapphire, this was the first time in the series that we had the legendary Pokémon actually play a significant part in the storyline, and the villains were trying to wake it to work with their plan to make the world full of more land or water. And after that, we had games like Diamond and Pearl, and Black and White, and then afterwards Black 2 and White 2, all of which had storylines of the villainous teams wanting to use the legendary Pokémon for some purpose or another.

So my question is this: do you think that RSE were the first games in the series that really showed directions for Pokémon storylines to take major directions forward? If not, which game do you think was the first that would do that? Discuss.

That's interesting to say - perhaps you're on to something here because yeah, this was the first gen that the villans had a "clear" plot - well, Team Rocket basically did all sorts of random stuff for money, but never really had a "definite" goal that will spell world domination for them.. but yeah, Archie and Maxie had a solid storyline to try and sieze control of the legendary pokemon's power, with the future Gens leading example to this: Cyrus wanted Dialga/Palkia, N needed Reshiram/Zekrom, etc, etc.

Yes.

Still, also no. Because even though Hoenn's teams had some kind of new goal, and Sinnoh's team had a very sinister and bigger goal, it wasn't until Unova that the evil team became something more than just bad guys to beat every once in a while. Unova was interesting in that sense and imo the first actual deeper plot.

Nah not at all. R/S/E's plot is pure B-movie material. Two dueling death cults summon ancient kaiju that put a city in jeopardy and you summon a third kaiju to deal with it. It's Godzilla vs. Leviathan vs. a giant killer whale. Awesome, but not very deep, and it's played for comedy every step of the way, from hilariously stupid grunts to team leaders with very stupid goals. I think when Diamond and Pearl it started getting deeper, with a team leader that was actually evil and the actual end of the world being a threat there instead of alternating sunshine and rain.

I dont think you guys are giving Team Rocket enough credit. Secret hideouts, kidnapping Pokemon, kidnapping people. They wanted to rule the world by controlling all the material goods.
And they were much smarter then for instance Team Galactic, which consisted one truly bad guy and bunch of idiots who were given orders they themselves didnt understand.
And it's the same thing with Hoenn. Two groups trying to control the legendary. They didnt just try to control a legendary, they tried to change the world, ecology and the entire planet by controlling the certain Pokemon. You have to awaken the legendary Sky Pokemon to stop the fight. I mean sure, it's a bit clique, but its far from shallow imho.