Hmm, tough one. So I'll ramble on points I jotted down on every so often over the last couple hours between work!
The first two gens are probably the most simplistic. The first game has you training to become a champion, and meanwhile you fought TR because Giovanni wanted power/money via the Game Corner operations, Siph takeover, etc and by exploiting Pokemon. And in GSC, you fight people trying to put TR back together by (besides cutting Slowpoke tails) experimenting with radio waves that forced Pokemon to evolve, and then taking over the radio tower to both exploit this and call their former leader Giovanni back to help them lead again.
But I don't think this is a bad thing. Sure, it's not the deepest, but it's decently done, it's understandable, and there's a clear plot and motivation for both TR and for stopping them. Throw in some touch ups and details in HGSS like more from Silver (including that Celebi event) and some more for the Ho-oh/Lugia parts of things (plus Eusine and Suicune extending across both regions!), and I'd say it's actually pretty well rounded.
RSE... I will agree with flight that the base for it is great. We have two different teams that are basically eco-terrorists fighting to in their mind help the environment! You have grander events too - you climb volcanoes in a race to stop them erupting, you travel under the sea to chase a hijacked submarine, you even have legendary Pokemon directly involved in the plot! That's actually pretty darn good.
The downside however is the execution of the bad guys' action. 'I'm going to erupt the volcano with the energy of this meteorite, and this will help the environment! (Even if they were team aqua).
Uh... what? I'm sorry, things don't work like that, not even in the logically inconsistent Pokemon world. And then there's fallacies in groudon/kyogre as well (hotter conditions will evaporate water... forming rain clouds, while making more rain means you're needing to take that rain from land-level water anyways...). As grand as it tried to be, even as a kid I was not convinced.
Fair play to the remakes in ORAS tackling these issues. Not only is stuff expanded on (mega stones, Steven, etc), but stuff is changed. There's more difference between Magma and Aqua now (as well as their respective leaders!), Mt. chimney isn't planned to be erupted, etc. Sure, some things could be improved yet, but this was much more well rounded, so ORAS may actually get my nod. In part because they also added that additional Delta episode which is pretty darn awesome with events too, and Sea Mauville and the additional elements associated with that were fantastic additions. More story telling like that, please!
DPPt... they were alright imo overall. Cryus' plan is pretty darn extreme, but I could believe his motivations and how he basically lead his grunts blindly behind creating a new world... different to the one he wanted to make anyway. The build up was fine, and Platinum also rounded things out a bit better, along with new characters (Looker!). This story was more grounded if you ignore the finale than the RSE plot events were imo, which can be both a good and bad thing.
BW is right up there. Yes, it also has a number of flaws, but I feel that it was the best effort until *maybe* ORAS, and it did one thing better than the hoenn plot did in involving characters. Nearly every Gym Leader was involved, and the theme of Plasma's ambitions was around from the beginning. N I disliked as a character, and how the story was presented at times was too one-sided, but compare it to other games and how you first learn about their respective groups. TR grunts... steal the Dig TM, or cut tails off some dim-witted Pokemon. Not much direct relation to their grand plan. RSE - guy tries to steal Devon stuff, which is related to an aspect but you don't quite get the team's major ambitions from those incidents until finally you get to the museum. It goes on. Here you first encounter them with Ghetsis giving a town speech telling everyone what Plasma wants! And as silly as the final surprise was (and annoying how they had mentions of
hacking the PC system yet doing nothing with it - that's a great plot idea!), it was a fine way to end things.
B2W2 may be more 'epic', but it was a worse story imo compared to BW. Your rival was just plain irritating and painfully obvious with his motivation and interactions with you. Using a pokemon-powered ice cannon is cool... but nothing much then came of it! And then stuff got a bit too muddled...
XY. Well, frankly this was disappointing. Again, like RSE it had neat basis for themes. But it was so darn condensed. You battle the big bad three times between the 7th and 8th gyms! The ending is so ridiculousness I had to laugh at it. Unlike BW, the rivals were all plain unlikeable despite being made to be nice. The Gym Leaders... well, unlike BW/B2W2 I struggle to remember more than a few names because most don't offer anything to the plot or even appear outside of their gyms and be noteworthy in said appearence (something that at least a couple Gym Leaders have done per game since gen 2... well, RSE wasn't great with it either to be fair. ORAS did better with e.g. Wattson). It's just frankly a mess.
Epic? It tried to be, but the execution is all over the place. (And then there's more obvious flaws. This well meaning leader has a set up that only the rich will be able to survive and enjoy a new beautiful world. That's not a beautiful thought at all, yet this appears like a plot hole rather than a feature.
Then the professor speaks about how passionate he was, honhonhon. Despite his attempted genocide.)
So... uh. tl;dr - Kanto/Johto games - simple but imo actually pretty decent with the stories, because they're sensible and believable.
Hoenn - RSE lacked in execution of the plot, ORAS did well to address many aspects and flesh it out.
Sinnoh - actually fairly solid overall imo.
BW - great attempt at involving many more characters and sideplots into the story and being consistent in its pacing. B2W2 - grander attempts, some neat themes but less enjoyable for myself due to rival/some plot points.
XY - potential but alas, so much wrong with the execution, plot and supporting characters.
tl;dr again - ORAS or BW imo.
I'll ramble about what I know of spinoffs some other post. Because you know I have something to say about Colosseum at least. Got work to stop procrastinating on. =p
