I have so many from 5th generation. My top 25 favorite Pokemon are from Unova.
I love the 2 cats (Purrloin and Liepard) and the 7 mustelids (Oshawott's evolution line, Patrat/Watchog partial mustelid one of the 2 animals they are based on are, & Mienfoo/Mienshao) from the region.
Rest in order from #1 to #25: Liepard, Watchog, Patrat, Dewott, Mienfoo, Mienshao, Purrloin, Emolga, Oshawott, Samurott, Servine, Snivy, Serperior, Reshiram, Minccino, Cinccino, Pansage, Pansear, Panpour, Simisage, Simisear, Simipour, Maractus, Zekrom, Swanna.
As for the game and poll, should have added one that says "All of them", generation 5 games are my favorites. My team in Black 2 and White mostly consist of my favorite Pokemon based on what the Pokemon looks like instead of a good team based on moves and stats. I'm going to struggle with Elite 4/Champ.
To answer the question: my #1 favorite at the moment is Watchog.