When I first bought Pokémon X when it came out I was tempted to get a Fennekin as my starter, but I figured all my friends were gonna get it too, because it seemed like it would be a popular choice at the time, so I decided to go with Froakie instead (Chespin didn't really interest me at all). As it turned out that wasn't the case, and Froakie was the more popular one, but oh well. I stuck with Froakie anyway, and it was a good thing I did.
Because I have this thing of keeping my starter Pokémon in my party as I play through any Pokémon game (I always thought it was a requirement, plus, well, gotta keep your very first Pokémon with you!) I found it to be growing on me, and after playing with it in Pokémon Amie I began to like it more and more. Once it had evolved into Greninja I think that was the turning point where I was convinced it was one of my absolute favorite Pokémon.
The big reason for me loving Greninja is that it is a frog, and frogs are my favorite animal, but the ninja part of it also greatly appealed to me. Reason being is I often consider myself a ninja because I have this thing of being able to move through a room unnoticed and walking up to a person without them noticing me there until I say or do something to get their attention, oftentimes startling them. It's awesome.
I should also add that Greninja was the only generation VI Pokémon I kept in my party. I think that says something, too (although technically I did have a Litleo in my party for a while, but it was eventually swapped out for a Flareon anyway so I don't think it counts).