Dang, this is hard because Kalos has one of the most beautiful dexes ever. I love gen 6 Pokemon. I will try to get it to no more than 5, but it won't be easy.
Goodra is really adorable. Dragonite has been my favorite Pokemon for years and with Goodra I felt like I had him reincarnated, the loveable giant. But Goodra still had a personality of his own I felt. He was an ugly duckling figure and I thought he was a good fit on the team of the nervous Shauna, expressing her well. I also liked his unusual method of evolving. Just like I feel about Milotic I think you should have to work hard for the things you want. And this is one whimsical Pokemon and has an insane coverage pool. I play more defensively so I really liked his great bulk and overall stats.
Greninja. I really loved all three of the Kalos starters at a glance, definitely in my top 3 favs. It was such an imaginative and progressive take to tie them to the medieval history of the land we uncover in the course of the story by making one a knight, one a witch and the other a ninja. I was sure I would pick Fennekin at first...and then I saw the final form. I thought delphox was actually cool, a fire fox sorceress wow, but hot damn...I want this sleek, acrobatic poison dart frog with a tongue for a scarf. I have never seen a design that fun before, and he has one of the most beautitul shinies I have ever seen. I hope to acquire myself a shiny Greninja some day. When he got protean he just got even better. He was always great with his speed and mixed attacking ability, steamrolling everything in my path as I journeyed through Kalos, but with his hidden ability he became one of the most fun and versatile Pokemon you could use.
Charizard, either form but I choose Y. I wouldn't have counted him but you said megas can be included (sorry Hawlucha, now we lost your spot) and what can I say? I have always been crazy about Charizard from the anime, I love his design and his big personality on the show. He is my favorite starter Pokemon of all time because of the colorful way he was portrayed in the series over the years, and it always made me want one games, whether he was the best choice strategically or not he was the most nostalgic choice. However. along comes Pokemon XY offering Charizard a fresh start where he can no be as powerful as he is portrayed in the anime i couldn't even contain my excitement. I picked the Y mega because I am a double orientated lady and love that sun support. I also felt Y was the one for me because his status as a special attacker and physical appearance seemed to be amore natural evolution for Charizard, but both megas are great. You can't go wrong with either.
Florges, a great special wall with great movepool and a great wholesome design. Florges is just beautiful, and it was fun colldcting the different color variations of this Pokemon like Vivillion. It was the first fairy Pokemon I caught, so she was my introduction to the world of fairy and opened me up to the idea of this strange, new time.
Pangoro. I love wildlife and pandas, and have even seen them up close in preserves. I love his disposition as the grumpy protector and saw him as always having my back. He was the first Pokemon I got to max affection, and he saved my tail from Siebold. I did not have a hard counter to his Gyarados. I should have picked up Helioptile, I liked him, but I could not afford to run another Pokemon with a fighting weakness. I usually could check water types with a grass move from Florges, but that won't work with Gyarados. I couldn't one shot the thing, and he got dragon dance up and the situation almost got out of hand. But because Pangoro loved me I got the in battle effects of affection, and it was able to take a hit that would have normally k.oed him as if he had a focus sash, and counter the Gyarados right back. I have so many cool stories of my pangoro, floating around with him in Olympia's gym,immune to all the psychic moves and exploring the beautiful dark of glittering cave, letting him hang out with my Absol so he could evolve. My Pangoro even k.od a lunatic cab driver in Lumiose City who attacked me because I couldn't pay him with a Pokemon level higher. It did not matter, my warrior panda would never let anyone ruff me up. He's a cool Pokemon.