Treecko - Treecko is cute and athletic, and has an adorable voice in the anime. Grovyle is a great character in the anime and in PMD: Explorers of Time/Darkness/Sky, and it gets Leaf Blade, one of the best Grass-type moves ever. And Sceptile has an awesome Speed stat of 120. But overall, the entire line has been designed with lots of effort.
Mudkip - Mudkip is one of the most adorable Pokemon ever, and it's plushie is one of my favourites. Marshtomp deserves props for being the cutest midway evolved starter since Bayleef. As for Swampert... Awesome design, great typing, great stats, and very fun to use in-game.
Froakie - Froakie was always my favourite Kalos starter, ever since I saw it for the first time. In my opinion, it's also the cutest Kalos starter, especially in Pokemon-Amie! When Frogadier was introduced, I became even more excited to use the Water starter. In Pokemon Y, it was the most badass Pokemon on my team, especially when it evolved into Greninja. Gotta love those epic frogs <3
I also like the lines of Bulbasaur, Charmander, Squirtle, Cyndaquil, Totodile, Torchic, Snivy, and Fennekin. However, I only felt like explaining the most notable ones :P