I made this from the least to the most. Keep in mind that Generation I is placed special in my heart so normal order will not work for them. And 'Least' doesn't mean its the worst.
Generation I - I placed this generation as the special one mainly because the fact that this is the generation who started this all. The Pokemon looks good, maybe because there aren't any pokemon to compare to begin with. And their team recket are the only criminal team that doing criminal thing for the sake of profit.
I admit there are lacks in the story, graphic, and tons of bug. But I must remind you that this is mainly because technological limitation. Satoshi Tajiri and Co. starved themselves for the creation of this generation. No matter how unoriginal some generation I pokemon look, I'll never call them 'uncreative' just to fend off raging nostalgiafans.
Now, the real order start
Generation V- I must say Generation V is my least favorite. Mainly because there are many polar opposite of many things. Before post-story there are many things to do mainly because the story, but after post-story, there isn't anything left worth to do. Some of the gym leader have terrific design, namely Burgh, and Lenora. On the other hands, there are some gym leaders with horrendous design, namely Skyla, and Brycen. The same also goes with the pokemon. There are pokemon with great design while the other are to horrible. These polar opposites prevent me to place it not int the least category. The story itself is good, but the overhyped reputation and the overrated character, N, prevent it to help itself. And the fact that many features from HGSS are not present makes me even more disappointed. At least, if it contain the elements from HGSS, Gen V will be placed more atop. Maybe if the remake of R/S/E or Grey really coming and satisfying enough, Gen V might be placed on top.
Generation II- Alhtough this generation are closely linked with the generation I that I loved, personally myself doesn't have many memories with this generation except how much I admired the famed Pokemon Suzaku, Ho-Oh. Other than that, I don't do much everything with gen II but it at least didn't disappoint me since it have many new features introduced namely breeding.
Generation IV- This generation save itself because the existence of HGSS. The fact is many of original content from Gen IV looks terrible. In pokemon department, many of their design are to ridiculous as well as their cry. The protagonist costume before the release of Platinum are also look terrible. But I must admit that Pokeapps have some useful tool like step counter, and the great potential of the story although have some lacking in many part, I take it as positive point of Gen IV. HGSS, the remake of classic GSC are the one that make this to the second top. There are so many improvement in this game. The new UI are really convenient. the "Follow Me" feature atlhough it is unnecessary, still a great addition. The remixes of the music sounds perfect. I even dare to says that the music in HGSS are the best in the series so far. And what I most like is the redesigned gym leader and the four executives. Many of the gym leaders have terrific design now, namely Morty, Pryce, Jasmine, Blaine and Green. Archer, Petrel, Ariana, and Proton also looks very good. The thing that HGSS lack is, the story. The story are still lacking like the previous game did.
Generation III- Originally this generation gonna be my least favorite, But after saw through all of Hoenn Pokemon, this generation so far offer the best Pokemon(Or the most fitted with my vision of pokemon). In term of design, some of them have good mix of realism, and not too cartoonish either. There aren't hardly any pokemon that looks too ridiculous. Their cry also seems perfect blend of pokemon-ish cry with real animal sound. Not like the future generation that sounds too realistic and past generation that sounds too....'8-bit' maybe? They also the first generation to introduce 2 criminal team at once with one similar goal or motivation: Eco-terrorism via legendary pokemon exploit. Although the potential is kinda wasted with regular bland story of the story. And there are Pokemon Contest, the side game which I like most after pokeathlon, get introduced. Also Battle Frontier introduced in this generation.
Here I also got my remake of generation I, FRLG! The remake really improve everything that generation I and R/S lack for. Although the story department still lacking. There are many radical change in Generation III(namely R/S/E), actually. Whether its mechanic, pokemon, or the story. It's too radical that maybe the pokemon fans are not ready for this scale of change. Again.