I guess my list would be 1>2>5>4>3 Walls of text incoming
1) In all honesty I'd have to say Gen 1 is my favorite. A lot of that is purely nostalgia, because I was 7 years old, and this is the game that got me into gaming and arguably where I am today as an artist, but at the same time I really loved the Kanto region. It was simple, it has enough branching pathways while retaining linearity, and the Pokemon were great. I loved the soundtrack in these games, and even today I still listen to that good 8-bit noise.
It introduced Red and Green, my two favorite characters in any game series, and Team Rocket, IMO the best evil team we've ever had. The story had its dark moments, but at the same time I really didn't notice those elements until I was older, in fact Lavender town was my favorite place, now the creepy vibe from it kinda [and, you know, the fact that the chandlers are all possessed and one asks you to give it blood] spooks me out.
The only real negatives that I can think of for it is either the high level of difficulty you have getting past the first two gyms if you picked Charmander, [something I never did], or because, when I look back at it now, the game moved so unbearably slow. Grinding in that game was a tedious mess and just trying to walk to the next town could take up to 5 minuets depending on the route. I think emulation has spoiled me a bit on this though. Overall though it was the perfect start to the series and will never be beaten out -6th gen is starting to come close though-
2) Gen 2 was the best sequel a game series could ever ask for. We got a whole new world to live in, and a nice amount of old Pokemon while mixing in some of the new ones. It even expanded on the story from Kanto, the story of Team Rocket desperate trying to reconnect, and what happened to both Red and Green after the events of RBY.
It also was the first generation with animated sprites, the ability to play as a girl, and the day and night system, things that looked so advanced to us as kids. The new land of Jhoto also had its fair share of branching pathways, not as much as RBY but it was still good. I was also pleased that there wasn't really many water routes added. Surfing was one of those things that I just really didn't like going, and not having to do it was so relieving. Silver was also a really good rival, having more development than Green did and more of an impact post game. We got to watch him grow from a thief, like his father, to a strong trainer. Granted we didn't really learn about any of this till HGSS It still presses the point of character development.
It also brought Steel and Dark types, the former being my favorite type of Pokemon. It also gave us the special stat split where we had special attack and defense. This helped a majority of the balancing issues that were wrong with gen 1. We also had the first addition of new types of Pokeballs. While a lot of them were either bugged or wern't that great, there were a few that worked well enough for the investment. We got Pokemon breeding, a whole new in depth idea for us to explore and has been greatly expanded upon to this day. The last major thing I think I should touch on is the addition of the EXP bar. I know it's a really minor detail but it makes it feel like grinding is going by so much faster. You were also able to just click on an object, like a tree, and have your Pokemon use the HM instead of having to go all the way into your party to select the move.
One downside was the clock system drained the internal battery like a mofo, luckily my Silver still works, and I felt the Kanto part of the game dragged. It almost felt too huge. We did however get to see a bit of character development with Green, something I was really happy about, and battling Red on Mt. Silver was the best way the game could ever end. I'd also say the pacing was a bit off. You tripped through the game at a really low level, but it got insanely hard once you faced the E4 and on. This game also suffered from the same problem RBY did, by moving so slow. Now granted this game did go by a bit faster, but it was still noticeably slow. One last downside was that there was no Safari Zone, at least not till HGSS.
3) Gen 3 is where things started going downhill for me. I'll start out with my positives and say that the Pokemon in this game were some of the best Pokemon we've had. They were all so...different. Exotic, and like creatures we had never seen before. The color pallet was also a nice choice. I liked how bright and vibrant the Advances graphics looked like compared to the really glaring colors in the Game Boy Color. Hoenn was also and overall beautiful region. There were some areas that I disliked about it, and i'll get to those later, but the towns and the routes were all vastly different and nice to look at.
I also liked having Secrete bases. While it's not a huge part of the game, it was fun to customize a room with things that you wanted to, and I hope they revisit this idea now that we have 3D graphics in Gen 6. I would love to sit in my base with my friends and just chill. I also liked the 2 choices of bikes, it was neat and interesting. And that about all the positives I can really list...not onto the negatives I have.
I was fine with not being able to transfer Pokemon over. I had never completed the Pokedex and hadn't even transferred over from gen 1 to 2, I didn't have a second gameboy or any cables seeing as how I didn't really have friends and no one in my family plaid Pokemon either. It was more or less the region and story itself.
The story was rather...out there. The whole team Magma and Aqua thing, while cool, really took me out of the experience. I liked Rocket cause I could relate them to real life criminals, I had a clear reason to dislike them. Here, I have mixed feelings towards both teams, I didn't really hate one or the other and by the end of the game they ended up accepting their differences and resolving the issue. The story all around just makes me feel...odd? I guess being a 10 year old and stopping a war between gods is a bit far fetched, then again so is a 10 year old taking down an evil organization...twice.
Also in terms of the story I feel the beginning part of the game, at least up until Slateport City, really dragged, and I mean REALLY dragged. It's hard for me to even go back to playing the game because it feels so slow. I liked the graphics for the most part but, it felt lacking. It also didn't help that I really disliked May. I didn't like her in the game and I hated didn't like her in the anime. In fact, where IS your rival in this game. This generation is where I like to say that rivals stopped being rivals and started becoming friendly competition. You hardly seen May or Brandon, and Wally was a huge pushover.
Where were the animated sprites [talking about R/S] and where was the day night system we had in the previous games? It all felt like a step backwards to me and is probably why, if I had to choose, Emerald is the preferred version. I also really didn't like the OST in this game. I've never been a fan of brass instruments, [and is a reason why I didn't like Skyward Swords soundtrack] so most of the time I ended up playing the game on silent.
And the surfing UHG the SURFING. I hate water routes, and this game is littered with them. It's another point where I almost get to bored to even keep playing . Its just this large mass of nothing and,unless you have a bunch of repels, you'll be running into a Pokemon every 5 spaces. Diving was fun, but it only held your attention for a really short amount of time.
Fire Red and Leaf Green were good remakes, but that's the thing, they were remakes. In all honesty these are 1 out of 2 games in the main series that I have never beat, simply because, every time I play it I end up just switching back to play Blue. The things they added were really nothing to get me excited over and I can't find myself getting into them. I make it to the S.S. Ann and then just put it down. I also, again, had problems with the music. I just couldn't get down with the remixes we got.
4) Gen 4 was when I started getting back into Pokemon again. Before then I was running off of Gen 1 and 2, with Gen 3 being put in the back of my mind. The transfer to the DS was honestly an enjoyable one. The graphics looked even better, and the region itself was just wonderful. I loved most of the Pokemon that you could catch and had a blast. I guess I don't really have much to say because those years of my life have kinda evaded me to be honest, and I haven't went back to play gen 4 in a long long time. There might be a reason behind that, but at the moment I can't really remember. I will say that Galatic was kinda a meh evil team as well and the game, especially in the beginning, had a bit of bad pacing. But overall I liked all of the gym leaders and areas. There was not much to complain about.
Heart Gold Soul Silver however was what really kicked me back into Pokemon. Again, yes, this is a remake, but this was a GOOD remake. It brought back the day and night system, and it even gave us Pokemon that follow us around. It also made the world brighter and Kanto didn't feel like some boring added on sidequest. The Safari Zone was put back in and the Red battle was just as epic as it was before, if not more now that we could actually see the environment around him.
5) I was now back on my Pokemon high and so excited for gen 5. I got it with my friends on the same day [Pokemon Black] but then, I stopped, yet again. Take everything I said about RSE and shove that aside, if were just looking at single games Black and White were the weakest games in the series. There were no old Pokemon, the level gaps between gyms was huge, grinding in this game was downright terrible and the story was just...bland.
I really disliked Bianca and Cheren, and the only character I ended up really liking out of all of this was N. The region, while nice looking, was so linear that at points it was just straight paths, and the competitive OU went to shit [granted it happened more in BW2]. I felt cheated. I was so excited for these games, running off the hype of HGSS, but it came crashing down.
This is the only other main series game I haven't beaten to this day, and I don't plan on it, because I've tried. There are so many things wrong with the two games imo that I could sit here all day, but I will add that gen 5 has the weakest cast of Pokemon thus far. I really only liked a select few and that was even harder for me while playing Black and White where 5th gen Pokemon were all there was in terms of selection.
I was skeptical of Black and White 2, I didn't really know how to feel about a second game. I guess the thing I was running on was that there were older generation Pokemon. I did pick up the game on release date and I played it off and on. I finally ended up putting that game down to, it wasn't until February of this year that a friend of mine convinced me to pick the game back up, and I did.
Then, for some reason, I liked BW2. I was able to finish the game and I ended up becoming interest in competitive Pokemon again. I admittedly still can't play Black and White, but the sequel is by far the better game, and I now have a respect for the Unova region. While I still felt the story of BW2 was weak the gameplay was what hooked me. I still feel the level spikes between the gyms was still bad, but I managed to get myself through. I also ended up picking up White 2 and i'm now playing through that one with a different team.
So far I am really hyped up for X and Y. I feel this will be the best of Pokemon and may even rival gen 1 as my favorite game. I really can't wait.
End of wall of text, Christ this took me an hut to type up. apologies for all the typos that are probably littered around,it's 4 am and i'm a bit lazy to go over it a 4th time.