For me it's tied between gen II and gen III .
The Johto region is by far my favorite region cause it has some of the best looking Pokemon (Ampharos and Umbreon being my favorites) and introduced breeding, day and night, and Dark and Steel types. I love being able to explore Kanto again and get the 16 badges. There is also tons of extra features which is why my Gold is my most played Pokemon game next to my White version.
Gen 3 mainly because the graphics improved a ton compared to G/S/E , they introduced really good Pokemon and with FireRed/LeafGreen , a large variety of obtainable Pokemon. Plus FR/LG brings me a lot of nostalgia since Red was my first game. Gen 3 also introduced some of the best features like Running Shoes which are very useful, contests which are really fun, and the expansion of berries which make battling easier and also more challenging.
Gen V is too new for me to call it my favorite, but I really like how much effort they actually put into improving the series and the storyline/features are just amazing. There are some Pokemon I'm not a big fan of, but I'm starting to get use to all of them, just like I did in Gen IV.