Leafeon - It's my absolute favorite Pokémon, next to Latias <3 I discovered my love for Leafeon last year, it's design and everything else just spoke to me so much...when I started my AS playthrough I asked a friend to give me an Eevee egg and I raised him up all the way through the whole game :)
Shaymin - I loved this guy ever since I watched Giratina and the Sky Warrior. I absolutely loved its Sky forme, and the fact that it was voiced by the same person as Tails, who's my favorite Sonic character :D
Tropius - One of my favorites from Hoenn, just love its design so much; it's definitely in my top 15 favorite mons :P
Treeko line - I always pick the fire starters, but Emerald was my first game, and I remember these guys very fondly. Love their designs as well.
Chespin line - I've become more and more fond of Chespin ever since I started playing Super Mystery Dungeon (Chespin's my partner)
Skiddo/Gogoat - Skiddo's such a cutie, I love it so much :D I love riding them in XY, as well
Snivy line/Cottonee line/Petilil line - These three lines have among my favorite designs of Gen V. The latter two's final evolutions are especially adorable <3
Other grass Pokémon/lines I really like- Oddish line, Hoppip line, Celebi, Chikorita line, and Cherubi line. I'd also like to vote for the unlisted Deerling :)