Favorite
Originals
Red (赤), Green (緑), Blue (青), and Yellow (ピカチュウ) - Yes, I'm talking about the original Japanese version, not Nintendo of America's dubbed Red and Blue. This game took everyone by storm. It feels good playing those game. Decent plot where Team Rocket tries to take over the world, Nice soundtrack, and decent gameplay. These Pokemon are actually good.
Ruby, Sapphire and Emerald - My most favorite of the series! It took a huge step forward after Gold and Silver with better changes such as the Berry mechanics, and introduces Nature, Ability, and Double Battle. Grinding is a breeze after defeating Norman which is your father depending on which gender you are. Good gameplay, awesome soundtrack, Nice plotline, and Good Pokemon. Hoenn was separated from Kanto and Johto, which is a good thing, because otherwise, it wouldn't have been good.
Remake
Heart Gold and Soul Silver - DISCLAIMER! Before you call me a hypocrite for liking this game and not the original. I have to say this: It's an improvement of the original. Just because the original isn't good doesn't mean that this remake won't be good either. *Clears throat*
Heart Gold and Soul Silver took a huge step forward after Fire Red and Leaf Green, with new features such as Pokeathlon, and Safari Zone (that didn't exist in Gold, Silver, and Crystal prior to Black and White), and mechanics which originated in Ruby, Sapphire, Emerald, Diamond, Pearl and Platinum. The plot was enhanced which unlike the original where you have to fight them, in this version, you have to fight them after taking on Clair, the 8th Gym Leader, they are actually harder, not the annoying kind of hard unless you're under leveled. You are allowed to have Pokemon that aren't in the Johto Pokedex unlike in FR and LG. We have Kanto, but thankfully, it's the way it's meant to be with minor changes. After taking on Red, you are allowed to obtain the Kanto starters (from Prof. Oak) and Hoenn starters (from Steven Stone) and are able to capture new legendaries. OH! And they also have their mechanics which the IV stat gets passed down to their child. Overall, Heart Gold and Soul Silver are one of the remakes that are well put together.
Least Favorites
Original
Gold, Silver, and Crystal - Those games aren't as good as RGBY. The plot line was mixed to horrible. There was Team Rocket trying to bring back Giovanni to become the leader but failed miserably. Those Pokemon aren't good when it comes to concepts. The biggest flaw is that after you defeat the Elite Four, you then have to explore, you guessed it, Kanto. Kanto wasn't good at all in Gold and Silver. It got nerfed into being bland meaning that you can't access Cerulean Cave, and Seafoam Island. Viridian Forest is nothing but just a part of Route 2. The only version I have beaten is Gold (when it comes to defeating Red). I am not joking at all! I couldn't get past Kanto on Silver and Crystal. On the positive note, both Legendaries and the Rival are unique. The Rival is the ONLY thing I see that Gold and Silver has what Ruby and Sapphire doesn't. All and all, it's a let down of the series. (No offense, Gen II fans) It used to be my favorite of the series as a child, mainly because I didn't realize those flaws as a child. If it weren't for Kanto being nerfed, it would have been better than Diamond and Pearl, but no. At least this game isn't as bad as the spinoffs I listed.
Spinoffs
Hey You Pikachu, and Pokemon Channel - I have nothing to say about those two. Those games suck.