Here's how I rank them.
1st: Generation 5 (Black/White/Black 2/White 2)
The reasons why I always say this generation is my fave: it introduced a lot of really great Pokemon, very interesting and memorable characters, two very different pairs of games which tie up the whole story together, B2/W2's massive postgame content (probably the largest postgame content ever) and of course, the unique motive of Team Plasma. Seriously, there is just so much I love about Unova.
2nd: Generation 6 (X/Y/Omega Ruby/Alpha Sapphire)
This generation marked the huge leap into full 3D, and new changes to breeding mechanics that made obtaining competitive-tailored Pokemon easier than ever. Kalos was also a very diverse region in terms of environments and introduced some well-designed Pokemon, along with having a huge regional Dex containing loads of older Pokemon as well, allowing for flexible team building options. Omega Ruby & Alpha Sapphire were also great remakes, and introducing the handy DexNav which allowed getting good IVs and Hidden Abilities in the wild much easier. Also, I love how much cuter May got in her redesign.
3rd: Generation 4 (Diamond/Pearl/Platinum/Heart Gold/Soul Silver)
I liked Sinnoh for interesting Pokemon and mechanics, as well as all those evolutions of older Pokemon, but things started slowly until Platinum fixed most of Diamond & Pearl's major issues. Platinum was pretty much what D/P should have been, and would probably be the Sinnoh game I always go back to. Heart Gold & Soul Silver also did a great job by improving on the original Johto games while still bringing the nostalgia with it.
4th: Generation 3 (Ruby/Sapphire/Emerald/Fire Red/Leaf Green)
Not much to comment on FR/LG, but I do have to admit while the original Hoenn games were fun they still look like an unfinished job especially when compared to OR/AS now, but it was my first game so it holds memories. Plus, this generation was what introduced most of the mechanics we're now familiar with, such as abilities and natures, along with being the first generation in full color.
5th: Generation 2 (Gold/Silver/Crystal)
I didn't play this one so not much, but I'm not a really big fan of Johto.
6th: Generation 1 (Red/Green/Blue/Yellow)
Again, same reasons as Gen 2. I'm not that huge of a Kanto fan.