Since I had a hard time deciding, I didn’t really make a top 10, but just placed all my favorite Pokémons. Most are due to the design, but also a few for other reasons.
My all time favorite is Seviper (#336). Snakes are my favorite animals, and although I like Ekans and Arbok as well, Seviper is definitely my favorite. It’s complete design is amazing, and I’m glad I decided to collect those as well along with my Pikachu collection recently. I also discovered that all the cards designs are pretty on-point as well!
Others I like ordered by national index (so in no particular order in terms of favorite - some I like more than others, but these are all my favorite Pokémons):
#25 Pikachu: Although it’s not my absolute favorite Pokémon, it’s iconic, well-known, and the mascot of Pokémon in general. How can you not like it?
#65 Alakazam: As a kid I always had (day)dreams about magical powers (and being a Pokémon trainer of course 
), and psychic was one of those powers. And just like with this entire list I like the design of Alakazam as well.
#081 Magnemite: I wonder how we would react when we would have seen a floating magnet in the current gens. Would we react the same way as to Pokémon like Klefki? I personally really like Magnemite’s design, and apart from Pikachu I had Magnemite the most in my TCG collection (probably about 12 or so out of the ±1,000 cards).
#93 Haunter: I just love how they portrait him in the anime. Always cracks me up when I see an episode with Haunter.
#99 Kingler: I liked it every time Ash used his Kingler in the anime, and after I got pulled the holo Expedition Base Set Kingler card, I liked it even more.
#104 Marowak: That he throws his bone as a boomerang is cool, and it’s also kinda mysterious that we never see it’s face. All in all a great Pokémon and I was happy every time I pulled on from a pack. Oh, and the colors of the Alola version is pretty cool as well.
#132 Ditto: Well, I guess we all know why I like it, because of his design of course! power to change into any other Pokémon. I always imagined how overpowered a Ditto with photographic memory would be, being able to transform into any Pokémon it has ever seen in the past at any time in a battle. 
#141 Kabutops: One of my favorites in terms of design. Just look at him(/her?), it looks so cool!
#142 Aerodactyl: I like dinosaurs, I collect fossils (among other things…) and I like his design of course.
#146 Moltres: When I imagined I was a Pokémon trainer in generation I, Moltres was always one of my six Pokémon. It’s a legendary bird, majestic and powerful at the same time. And the WOTC 21 promo Moltres card is also my favorite card design ever.
#151 Mew: Mew is just cute ^-^, especially the giggle in the anime.
#185 Sudowoodo: It’s funny. I like that it’s pretty tall, and it hates water. And I also really liked the Sudowoodo flippo. I never really understand people who collects loads of the exact same card, but I did the same with this flippo as a kid. 
I probably had about 30+. (PS: Are they called flippo in English as well, or is it cogs or pogs or something?)
#208 Steelix: Just amazing looking, and I had quite a few Steelix cards in my collection. Also, my grandpa made me a Steelix painting once (with made up colors since he forgot what color it was:
. So it has green, yellow, red, etc.)
#319 Sharpedo: I love the Team Aqua’s Sharpedo card, which is the main reason why it’s on this list. I got it from a pack, and love it! Just like Kingler one of those cards I just love mostly due to one amazing card. When I had this I didn’t even knew it was actually ‘cut off’ at the end.
#384 Rayquaza: Apart from Seviper, Rayquaza is probably my favorite. It’s cool, looks great, his movements are awesome in the anime, he’s strong, he’s kinda a snake as well as a dragon. And he’s mostly seen above the ozone in space.
#462 Magnezone: A worthy last evolution of Magnemite. It’s just so smooth looking and one of my favorites of generation IV.
#632 Durant: Ants are one of my favorite animals as well, and they nailed it with this Durant design. And being a steel-type is also a plus for me.
#717 Yveltal: Another amazing legendary design, and great choice of colors. I didn’t really liked it in the movie, though…
#M-6 Mega Charizard X: Those colors! This is what Mega Pokémon is all about!
#M-142 Mega Aerodactyl: Added spikes are never a bad thing imo, so I like it just as much as the regular Aerodactyl.
#M-384 Mega Rayquaza: I like Mega Rayquaza as much as the regular one. And I also really like the Shining ones. And those ?whiskers? that corrospond with the yellow stripes on the regular version is a nice touch; like they came off from his skin.
#M-660 Ash’s Greninja: The star of the show in the last anime season.
#724 Decidueye: Maybe adding the Sun & Moon Pokémon is a bit soon, but some designs are pretty cool. I really like that he uses his wings as a bow and arrow.
#733 Toucannon: Ok, I hate the name. But what can I say, I love Toucans, and although it looks more like an actual Toucan than a Pokémon, the natural design of ana ctual Toucan is amazing, so so is this Pokémon’s design. 
He should just have been a bit less angry.
#746 Wishiwashi: What’s up with those names?!.. 
I like the way it’s scared alone and fearsome as a group, though. Probably my favorite of the Sun & Moon Pokémon.
ADDED: #778 Mimikyu: My favorite Pokémon after Seviper. I absolutely love how they portrayed it in the anime, and the entire vibe and story behind it. It’s also the third Pokémon I now collection after Pikachu and Seviper.
#792 Lunala: Well, you can say quite a few things about some Pokémon designs, but almost all the legendaries are pretty cool. It’s hard to name one that isn’t.
Ok, the list is a bit longer than I thought; and I even left out quite a few of them…
