Personally, i think it's:

1.Gen 3 (there's a lot of factors that made me decide this but the most important one is the very fast and smooth gameplay most GBA games had, and most DS games didn't (Gen 5 being one of the few exceptions, which is why that's my 2nd favorite))

2.Gen 5

3.Gen 4

4.Gen 2

5.Gen 1

(I know I'm gonna piss off a lot of genwunners with the Gen 1&2 placements, but i honestly think those games aged very poorly)

Best Pokemon game is Pokemon Emerald (Dat Content (Battle Frontier, Deoxys, etc))

NOTE: Gen 6 is excluded since it's way to early to judge.

5 > 3 > 2 > 1 > 4

1. Gen 5
2. Gen 2
3. Gen 3
4. Gen 4
5. Gen 1

3 is the best, then 1, then 2, then 5, then 4. After RSE, the games have gotten too easy, so they're immediately worse....to me that is....

4>2>5>3>1

Since Diamon is my favourite game of all time Gen 4 takes the top spot. Gold and Silver did so much, and are a lot better than the first games. The fifth gen games was really good, but didn't have the same magic as the previous titles, at least not for me. Gen three isn't one I've played too much, although I have beaten Emerald once. Pokemon Blue had it's problems, mainly balancing ones, and it felt aged when I played it (4 years ago). Still a wonderful game, and it deserves credits for what it have done, but it ain't better than the others.

While it didn't sound like it I actually took spin offs into account as well. Doesn't help anyone, I've probably spent close to 1500 hours in gen 4, with gen 2's roughly 150 coming in second place.

5>2>4>3>1

2 > 1 > 4 > 3 > 5

My favorite is gen. 2 and then gen. 1, so the remakes make quite a difference for me, cause without HeartGold and SoulSilver I would put gen. 4 last place :D

1.Gen 4
2.Gen 3
3.Gen 2
4.Gen 5
5.Gen 1

Depends on which games you focus on. I, for example, think that G4 was the worst gen unless you count the G2 remakes. However, if you count HeartGold/SoulSilver, you realize that they had pretty much everything that made the original games great and more, driving G2 further down the list.

My opinion:

Black/White > HeartGold/SoulSilver > X/Y > Ruby/Sapphire > Red/Blue > Gold/Silver > Diamond/Pearl

I haven't played the G1 remakes and haven't beaten Black/White 2, so I can't comment on them. However, I feel that the Pokemon games have, roughly, gotten better with time, with Diamond/Pearl being the chief exception due to its boring world and X/Y, despite being a perfectly fine game, being a lesser exception due to its stepping back from some of the things that made G5 great (lots of new Pokemon, interesting characters, cool themes, etc).

Talk about introducing one of the most debatable flame inducing topics! I like it!

1. Gen 2

2. Gen 1

3. Gen 6

4. Gen 4

5. Gen 5

*Never played Gen 5 (yet)