I've just recently played Omega Ruby, so here are my favs:
Zigzagoon/Linoone - I ADORE Zigzagoon's design, this scuffy little guy reminds me of a dog I once had growing up. And I really like Linoone too, in fact I took Linoone to the Pokemon league with me!
Poochyena/Mightyena - I love this tough pup and it's even tougher evo, great design!
Wurmple - Probably my favorite bug type, it's so cute!
Altaria - Probably my favorite flying type. So cute and fluffy.
Milotic - I think Milotic is one of the best, so pretty and elegant.
Absol - I love this one's design!
Breloom - I think this guys is so fun and has a great design!
Skitty/Delcatty - Of course these two are some of the cutest pokemon. Delcatty reminds of those 'lion cut' cats.
Mawile - Adorable and feisty!
Electrike/Manetric - I used to not like either of these guy's designs, but I had one on the team in OR and playing with it in Pokemon Amie really endeared me to this one.
Aron/Lairon - I think these two are really adorable, tough looking but adorable nonetheless, I loved coddling them in Pokemon Amie, they both reminded me of another dog I had.
Numel - I LOVE this lil camel, I adored mine on OR, I was a bit sad to evolve him to Camerupt since Camerupt wasn't a design I really enjoyed but that's okay, deep down Camerupt is still my little Numel.
Latias - I really liked Latias, I was a bit disappointed I didn't have one in OR but that's okay, Latios is great too.