For me, it's definitely Pikachu. It's the most original, in my opinion, and generally, it's a lot popular. There are many people out there that don't necessarily following Pokémon, but if you ask what Pikachu is, they'll be able to answer easily. It's our mascot, after all, and could go head-to-head with many other popular Nintendo characters such as Mario, Luigi, and Link (of course, there are plenty of others, but these are the only ones I'm able to think of right now, sadly). Plus, it's made appearance in almost each and every anime episode so far, which is quite an accomplishment, if you ask me.
My second favorite would most like have to be Plusle and Minun; they're an extremely adorable duo.