It's funny because in almost every intstance, my least favorite is the one I picked in my first play through of each. Ha!
I'd do this with a poll if it weren't for the max of ten options...
So in each starter set, Kanto to Unova, what is your least favourite in that set? Here are mine:
Kanto: Charmander line. Game only they are all equal in my eyes, the Squirtle line maybe taking 1st. However, this may sound cliché, but the way some (only a minority) fans harp on about Charizard, just gets to me. I did a Diamond playthrough with all three Kanto starters and you know who did the best? Venusaur (named Maryjuana), followed by Blastoise. Charizard was actually somewhat underwhelming.
Johto: Totodile line. Again a fairly close one. However I like Chikorita the most and Cyndaquil just edges out so sorry my little Croc.
Hoenn: Mudkip line. I no liekz mudkipz? Yeah, some of the starter designs irk me in this gen. Sceptile is awkward, Combusken is ugly as sin and I don't like the Marshtomp's or Swampert's cheek things. So it came down to (in game) performance. Swampert felt the most awkward.
Sinnoh: Chimchar line. God I hate Chimchar. It has a poop on its head for Pete's sake. Monferno looks fairly cool, but Infernape just returns to the ugly with its stupid armour stuff.
Unova: Tepig line. Another Fire-Fighting, awkward design, unappealing stats. The Tepig line pale in comparison to both Oshawott and Snivy.
Funny. I never disliked the Grass types.