General

Out of all the pokemon games, my least favorite is easily 6th gen. It was just too easy. Just through natural story progression, my Aegislash reached level 84 before battling the champion, and she was accompanied by a backup line of pokemon scattered throughout the upper 60s and 70s. The game feels shorter and lacking of content.
Of course, I'm not saying it's a bad game. Of course, it has a detrimental flaw in mechanics, but that isn't going to blind me from the upsides.
No longer being stuck to that annoying grid (!), and the enhanced graphics are all great. X and Y just feel like they had the potential to be so much more. I hope in pokemon (z?) that Game Freak fixes these problems in mechanics in gen 6.
Mega evolutions seem a bit forced as well.
Back to the main question:
1. Mechanics: 5>4>3>2>1>6
2. Storyline: 1=2> or =3>4>5>6 - I don't want to sound like a gen one elitist, but team rocket was and always will be the best team. Magma/aqua come close. After that, their uniforms became too ridiculous for me to handle.
3. Post-Game Content: 5>4>6>3>2>1
4. Pokemon Design: 1>3>2>4>5>6 Older pokemon are just more memorable.
5. Region: 1=2=3=4>5>6 I hate linear regions. The newer gens feel way too linear.

Ugh so much time to take thinking about this.
Let's see..
1. Gameplay mechanics, etc. 6>5>4>3>2>1 Each new gen brings improvements to mechanics as well as new ones that work really well.
2. Storyline 5>3>2>6>4>1 They sprinkled Team Plasma literally everywhere and I got to know a lot about them. Trivia: Colress's theme was written "all over the place" because Colress goes all over the place.
3. Post-Game Content 5>2>4>1>6>3 More is better. Just allowing access to certain legendaries is nice but I want to know more to the story. And because Colress can be battled every day.
4. Pokemon Design 2>1>3>5>6>4 Simpler designs are better and it's what make Pokemon look like Pokemon imo. 2 is better than 1 because it has more cute designs like Ampharos, Azumarill, Mantine, Jumpluff, and Furret.
5. Region Omg this is so hard... I can't really put them in a definite order. 2 and 3 for the maps, 6 for beauty, 1 because it's classic, 4 and 5 I'm not sure so they're among my last.

Let's see... probably:

[b]1. Gameplay mechanics, etc.:[/b] 4, 5, 6, 3, 2, 1.
[b]2. Storyline:[/b] 5, 3, 6, 4, 2, 1.
[b]3. Post-Game Content:[/b] 5, 3, 4, 2, 6, 1
[b]4. Pokemon Design:[/b] 5, 3, 6, 4, 2, 1
[b]5. Region:[/b] 2, 4, 3, 6, 1, 5

I've probably made some of these decision without much thought, but this seems about right, for the most part.

[quote=monty007]Ruby saphire remakes where?[/quote]

There is a BIT more evidence of those remakes. In the Lumiose Art Museum, there is a painting called Mr. Briney's Passion. It shows what I believe to be Mr. Briney's OLD ship in what I believe to be 3 dimensional polygons.

I can only do back to gen 3 for some.
1. 6>4>3>5
2. I don't know yet because I haven't finished 6 omg but 4>5>3 so far.
3. 4=3>6>5 most likely.
4. 3>>>>5>4>2>6=1 The first gen pokemon are actually kind of boring to me.
5. 3=2>4>6>5>1

1. Gameplay mechanics, etc : 6>4>3>5>2>1
2. Storyline: 4>3>2>6>1>5
3. Post-Game Content: 2>4>6>3(FR/LF/E)>5>1>3(R/S)
4. Pokemon Design: 6>4>3>2>1>5
5. Region: 3>4>6>2>1>5

I liked them all but I really dislike 5th gen.
5th gen felt like a filler and rushed or not complete.
Everything in 5th gen could have been waited and put in 6th gen.
5th gen also had its own exp rate thing when you fainted a Pokemon and no surfing required the whole game!
Even 6th gen I am kind of hating on the whole no surfing. It seems you only need it in 2 places and one of them could have been fixed by adding a bridge.
This is why I loved 1,2,3 gen since there was places to explore. 4th gen was my fav because of the storyline!

[url=http://www.youtube.com/watch?v=VuGBwqGhIh8]You gotta admit gen V's ending theme was the best out of all them[/url]

1. 6-5-4-3-2-1
2. 5-4-6-3-2-1
3. 2-1-4-3-5-6
4. 6-5-4-3-2-1
5. 6-2-4-3-5-1

Overall I think...

6>5>4>3>2>1. I honestly loved them all though

1. 6>5>2>3>4>1
2. 5>6>4>3>2>1
3. 5>2>4>3>6>1
4. 6>3>2>5>4>1
5. 6>2>3>5>4>1

Overall: 3 > 2 > 1 > 6 > 5 > 4
Sinnoh was garbage

1. 6>5>4>3
2. 5>6>3>4
3. 3>5>4>6
4. 3=4=5=6
5. 6>4>3>5

2,1,3,4,5,6 for all.

Gen 2, and more specifically the remake are my absolute favorites for pokemon design, and region. You just cant beat a game that has two regions.
Gen 3 for post game because of all the legendaries and particularly the unique way you had to get the Regis.
Gen 6 is my favorite for mechanics, the 3d is a welcome change

I'll just do an overall one.

2>4>3>1>5>6

1. 6-4-3-5-2-1
2. 3-2-4-6-1-5
3. 2-4-5-6-3-1
4. 2-3-1-4-6-5
5. 2-6-3-4-1-5

1. 6,5,4,3,2,1
2. 4,3,2,1,5,6
3. 6,5,4,3,2,1
4. 1,2,3,4,5,6
5. 5,4,6,3,2,1

Ruby saphire remakes where?