Gen three while I never played it, mudkip seems better than KFC or a lizard...
Gen four... I had piplup.. Got to the 6th badge... And was tired of no fire types aside from ponyta, so... I restarted and chose chimchar, even though I hate monkey pokemon as a rule of thumb... But I have to say, I have enjoyed it. And, coincidentally, the game seems easier with it.
Gen five, I haven't played it, but counting unevolved... I like teppig and oshawat. Shame in that gen, all the starts seem really well rounded when at max evolution.
I know the question wasn't favorite from each gen... But can I take them all and count them as one?
Fuhine.... I will say gen four. I didn't really care for the gen three pokemon at all really. None of them seemed to stand out and shout at me, but I did like a few.