Not only did it expand upon the previously best games in the series...It added tons of extra bonus things, and pretty much just made awesome everywhere. I don't know if there's a logical way to say what I want to say, but that's good enough.
Bonus:
Totodile and his evos. Best water starter, ever.
After Red/Blue, my expectations were high and Gold/Silver blew them away. And I can't tell you how kick ass it was to find out that beating the Elite 4 the first time was only like half of the game.
Bonus: I love me some Crobat! In almost every Pokemon game there's a Crobat on my team. Crazy fast and good at stalling while the opponent dies from poisoning.
I actually do plan on playing it in a few weeks, but there's no way I'll have enough time to go through the whole game.
Bonus Question: Kadabra for life.
That was before they started throwing too much shit in and made it too cluttered.
Bonus Question: Heracross.
I love Bug types, but they're never any good; not so with Heracross. Plus, Fighting is my favorite type, and he's part that too. Badass combination.
Bonus Question: The Ghastly/Haunter/Gengar evolution was one of my favorites.
Bonus: Charizard. Dudes a badass.
Bonus: Going to be lame but... Charmander and its evolutions are my favorite. Fire dragon/lizard thing is cool. Also Ampharos holds a special place in my pokeheart.
Bonus: Infernape. Flaming Monkeys.
I know 101 people are gonna say gen 1 and 2 but they need to realize that the game got better as time went on. Lots of good designs came in and lots of bads ones to just like in the first two games.
Pearl. Diamond and Platinum introduced
Online trading and battling which allowed me to easily finish my dex. Awsome game was Awesome
Bonus:
Torchic and his evolution Blaziken, to me that was the epitome of fire type pokemon before the disaster and disgrace with Chimchar and his evolution Infernape.
Pokémon Heart Gold.
Bonus Question: Gyarados.
BONUS: That is so effin' hard for me. I've always loved Eevee and all it's evolutions, Dratini & its evo., and Raichu.
Bonus: Charizard is my favorite pkmn.
After beating the Elite Four in Johto, jumping on the train and finding out you get to replay Kanto all over again was one of the most jaw-dropping gaming experiences I've had.
Also, squaring off against Red at the end of the game was pure bliss.
Bonus: Blaziken 4 lyfe.
BQ: Best pokemon would have to be Charmeleon.
Best Pokemon: Gyarados. It could totally kick Godzilla's ass.
Bonus: Snorlax.
Introduced key features such as day/night, and breeding. Also best in the series because unlike any other Pokemon game, when you beat the elite four, you realize THAT WAS ONLY HALF OF THE GAME! You get to go back to Kanto and do the most epic thing in Pokemon game history: BATTLE ASH! Plus gym leader rematches with leveled up pokemon, oh man I could go on forever. This is no contest.
Bonus: Arcanine, dog on fire...nuff' said.
Biggest reasons: Amazingly smooth new control scheme, more character given to NPCs, side activities don't suck, Cut isn't useless like it was in D/P/Pt, and actually deserving the DS as a console.
But...I also like Emerald a hell of a lot, out of the entire series, it felt the most balanced and you had a LOT of Pokemon to choose from (having two Pseudo-Legendaries didn't hurt either), and the introduction of the Battle Frontier made it my favorite, so when it gets down to it, it's really HG/SS's atheistic changes that made it the best.
Bonus: Metagross, it was the first Pokemon that truly scared me the first time I encountered it.
@MilesTailProwe
That's true, they did revolutionize the series with the introduction of online, and really expanded opportunities for players. If you had online, that is. If you didn't, the game degraded into half of it consisting of near-useless side activities, not to mention Diamond and Pearl being unbalanced as shit (Only two fucking Fire types? BIDOOF?!), though Platinum did fix many of these initial issues.
So Platinum
BONUS: Shinx - Luxray. Best first capture pokemon from ANY of the games - screw you Rattata.
I've got to give it to second gen, I think. The fact that they gave us both Johto, then all of goddamn Kanto in the same game is beyond awesome.
Best Pokeyman Ever: Vespiquen. SHOOT BEES. DEFEND WITH BEES. HEAL WITH BEES.
Now, I know that the third generation (namely Ruby, Sapphire, and Emerald) are often viewed as, well, the weakest in the entire series. I'd have to disagree, however.
Up until the release of Ruby and Sapphire, Pokemon ran off the same engine on the original GameBoy, as both the Generation 1 and 2 games ran identically. Due to that, I felt that the second generation of games (Gold, Silver, and Crystal) felt too similar to Generation 1, and there seemed lack of true variety in the play style.
However, with the release of the GameBoy Advance, Nintendo was forced to rewrite the entire system of the Pokemon series. Not only were the graphics and sound abilities change to match the system, oh no. The technical developments made behind the scenes are staggering. The third generation invented the metagame and paved the way for competitive play, which is a large part of the focus of Pokemon today (the 4th generation further expanded upon this, but it didn't feel quite as revolutionary).
The 3rd generation included many changes to the series that we are familiar with today (double battles for example), but all while showing us, in the case of FireRed and LeafGreen, that the original games could not only be remade, but also improved upon.
While the Pokemon may not have had the best designs and the game may have focused too heavily on water travel (too much for some people), the story was entertaining for your first playthrough, and the new introduction of legendaries eventually became fan favorites (Rayquaza, the Regis, Jirachi, Deoxys).
The fact of the matter is, each Pokemon game builds upon, and improves upon, the last. However, this was easier done for certain generations than others. Generation II simply added more features to an already-developed system, whereas the third generation was forced to completely remake from scratch. Using that as a foundation, I believe the fourth generation was able to truly develop as well.
So for me, it's Ruby and Sapphire that are the best, simply because it was something that truly changed the series forever.
As for the bonus question, Squirtle of course. Check my avatar; he's fly.
Bonus: Onix
Favorite Pokemon? Cubone. 'Nuff said.
Honestly, I prefer Gold and Silver (you arent considering the new ones the same vote I hope. HG/SS are a generation all their own) but HeartGold brings so much to the table, even if I dont like all of it, that's its hard to deny it.
Bonus: Snorlax. Because he's sim...simply....just....zzzzzzzzzzzzzzzzz.
Bonus Question: Ursaring.
Bonus: Snorlax, because I Sleep Talk all the time.

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