I don't like both Minun and Plusle but between the two,
Minun is my choice for the exact same reasons as Omega Soul.
Since my favorite type is Grass, my favorite Musketeer is also
Virizion. I don't like Cobalion because it doens't seem to have a hat, just horns, and because it's Steel. I like Terrakion but Aramis is also my favorite Musketeer so another reason to like Virizion.
About the Kanto birds, I prefer
Zapdos. Moltres seems like a yellow rubber chicken being cooked in flames, and Articuno seems like a frail bird, with Zapdos reminding me of Fearow (one of my favorite birds) and those black feathers are awesome.
Between Mewto and Mew...this is tough...I like Mewtwo because it has the same colour scheme as Frieza from Dragon Ball and they were both fierce but
Mew is more elusive, has more history and it's original, not some artificial creation.
My favorite Johto bird is without a doubt
Ho-oh, because it reminds me of Japanese traditions and it's also representative of Ecruteak, while Lugia seems like a fat bird with enormous hand and it's Psychic seems akward.
Raikou is my choice among the beasts because it has big fangs, a nice color scheme and purple hair that's better than the one from Suicune. Entei is Fire, so I find it almost impossible to like it.
Latios is better than Latias, because of the same reasons as for Minun.
I've always prefered
Kyogre to Groundon and Rayquaza, because Rayquaza has little history, and I find Kyogre more beautiful and better shaped (more aerodynamic) than Groundon.
Regirock is my favorite golem. I dislike Regice and Registeel's symetry is nice but its colour sprite in Hoenn was akward and made me like Regirock more. Also, Regirock has orange which looks nice!
Dialga beats Palkia and Giratina because it controls time and it doesn't have Palkia's high heels. I hate Giratina's normal version and unfortunately, the Distortion World version, while better, didn't made me like it more.
I hate the Emotion trio. Too bad in the anime J died because of those idiot creatures.
I like
Zekrom more than Kyurem and Reshiram because of its type and color scheme. Reshiram looks like a white Lucario with mutant angel wings and a car's exaustion pipe for a tail and Kyurem is nothing but a zombie shell.
I don't like the Kami trio.
Oh yeah,
between Cresselia and Darkrai...none of it. Cresselia is only the Crescent moon instead of the full moon which I dislike and Darkrai is way too simple.
Edit - updated with Seven is a Color's duos and Pikachu6319 note:
I'll go with
Xerneas every time. It's a deer (or another species akin), it's connected to creation and life (too bad it isn't Grass
) and it is symetric, which is why I don''t like Zygarde's body, despite the good colour scheme. Yveltal is just red and death.
Seviper always! Poison is my second favorite type, until HG I never had an Arbok and Seviper was a good replacement and surprise. Also, it's black with a lovely pattern. Oh yeah, and it has that fearsome look, fangs and tail! Adorable.
Again, until HG I also never had an
Electabuzz and I don't dislike Magmar but I don't like Magby and I dislike Magmortar. Electabuzz was a great companion in HG, I like Elekid's challenging look and despite not liking Electivire, it reminds me of Dr. Robotnik/Eggman from the Sonic series, my first videogame villain.
I never liked
Heracross in the anime due to always be eating Bulbasaur's nectar (?) but I don't like Pinsir long arms and I ended up liking Heracross' blue color.
My first Hoenn game was Sapphire so I was stuck with
Lunatone (funny how despite having Pokémon that I like, I would always ending up desiring those from the other version!) but I always prefer the moon to the sun.
And again, I was stuck with Sableye but desiring Mawile. In a recent Emerald walkthrough I found out that Sableye is a nice Pokémon but I prefer
Mawile because of that big jaw (I like carnivorous plants). Too bad that Mega-Mawile is a Mega and not an actual evolution because I just love the esign and how it looks like an ancient Japanese woman.
Throh/Sawk? To hell with both of them. They're hideous, horrible and a pain! Oni wearing fighting robes? WTH?
I never trained a Durant nor a Heatmor but I prefer
Durant, because of its design, type and because Heatmor is a Fire type (but with a nice colous scheme even in Shiny form).
I never liked Tauros' back sprite with that massive hump. I always liked it's whip tail, its horns and colour scheme. Perhaps I'll train one in B2, where the hump is less visible. So, I'll go with
Miltank because she's a happy and fat pink cow.
My Flying companion (post E4 but still a companion) in HG was Skarmory but I like
Mantine's elegant design and nice expression. My previous signature was a Mantine and I reccomend watching its XY animated sprite while hearing Jordi Savall's "mare Nostrum" because it really suits Mantine and it's peaceful.
I just love
Omanyte and Omastar (Omastar has that fearsome look but it deserves some love!). Kabutops reminds me of Scyther, a Pokémon that I don't like that much and Kabuto is just a brown disk.
Lileep and Cradily any time (well, in my first time (Sapphire), I chose Anorith because Claw Fossil seemed better than Root...it was LeafGreen that really drove me into loving Grass type). While Kabuto has red eyes, which I don't like, Lileep and Cradily have yellow eyes and remind me of that character from Final Fantasy and Jawas from Star Wars!
About the Sinnoh fossils...I don't like them to the point where I don't even want to think about which one I dislike the less.
Tirtouga and Carracosta because of the same reasons as Seven is a Color. I find them better than Sinnoh's fossils but Kanto and Hoenn ones were the best. I'm still hoping for an ancient relative of Yanmega for a fossil.
I also don't like Kalos fossils. Amaura is just a blue Meganium and Tyrunt is just theT-Rex fantasy come true so I'll pass both of them.
Spritzee/Swirlix: I like Spritzee but hate its evolution and I hate Swirlix but like its evolution despite looking like a dog with the tongue out, so I'll go with this last option.
Skrelp and Dragalge all the way because it's Poison and I also like seahorses. Though I wouldn't like to wake with one of those in front of me! Also, Clauncher has the same problem with Kingler: one bigger pincer than the other.
Last but definitely not least...between Lotad ans Seedot I'll go with
Seedot because it has a better shape, colours and it hasn't a derp (while kind) expression!
PS:
I don't consider Heatran and Regigigas a duo so I won't make a choice.
3rd UPDATE
Breedrill over Butterfree because Beedrill is a Poison type, it deserves little love and Butterfee seems more lika an evolution for Venonat than Metapod. Also, Weedle and Kakuna are better than Caterpie and Metapod for the same reasons except the last.
Nidoqueen over Nidoking because while I like Nidoking's purple colour, I prefer Nidoqueen female look, movepool and blue for a Poison type isn't common and Nidoking seems always angry Nidoqueen seems gentle despite being Poison.
Between Clefable and Wigglytuff...that anime Jigglypuff was annoying after a while and Clefairy are pretty elusive so I'll go with
Clefable as I like the whole line, from Cleffa to Clefable, while in the second line, I just like Wigglytuff and Igglybuff's red eyes are somewhat scary!
Ninetales over Arcanine because I prefer foxes (and cats) over dogs and Ninetales has elegance and mysticism while Arcanine has that China reference which I never liked. In the end, I saw it as a Japan vs China thing and I went with Japan. Besides, that sad and lonely Ninetales episode with Brock was amazing and only helped to like it.
Victreebell over Vileplume. I like both, I always liked James and Victreebell was his Pokémon and also the one I could caught (as a Bellsprout) in Blue and Leafgreen.
I choose
Hitmonlee over Hitmonchan. I never liked Chan's female look and I prefer Bruce Lee over Jackie Chan, despite this being good too.
Milotic over Gyarados, because Milotic is gentle and I don't like seeing Gyarados with its mouth always opened.
Ariados over Ledian because Ariados is a spider, it's Poison and has nice colours.
I can't choose between Espeon and Umbreon because Umbreon seems like a devil goat with those red eyes but Espeon is Psychich, a type I never really liked. That said, if I really had to choose, I would go with
Espeon because of its red jewel and body colour.
Murkrow over Misdreavus. I prefer Ghost way more than Dark but I just love Murkrow's concept and the area in which is found!
I'll go with
Donphan over Ursaring because Ursaring is too simple and angry while Donphan can be gentle. Also, I fell in love with Donphan after seeing its Roll-out attack in the 1st movie!
Dustox over Beautifly because of the same reasons as for Beedrill.
Pelliper over Swellow because I of their type and utility in S/R/E.
I don't Volbeat nor illumise but I'll go with
Volbeat because it seems funnier with its curly antenae and chubby body.
Sharpedo over Camerupt because I prefer piranhas and sharks over dromedaries and camels.
Huntail over Gorebyss because I prefer Huntail's deception over Gorebyss' and this one's pink is too much.
Leafeon over Glaceon because Leafeon is a Grass-type and I never understood what are those pointy thingg coming from Glaceon's head/hair.
East Shellos and Gastrodon because of its body colours and humps.
Stunky and Skuntank over Glameow and Purugly because the first are Poison-type.
Gothitelle over Reuniclus because it has a gothic and female look and isn't a green fluid blob (I like the concept but when comparing with Gothitelle it's another story)!
Excavalier over the Accelgor because it looks like a jousting knight and despite not liking the Bug-type, I like its concept.
Pansage and Simisage over Pampour and Pansear because they're Grass and Simisage has the most balanced body (not a fat belly nor a pointy dress)!
Petilil and Lilligant over Cottonee and Whimsicott because only of Lilligant's female and cute look, because Whimsicott seems more like the Gingerbread Man.
