How do you pick a version?

Gen 1: I got Pokemon Blue. I wasn't around for Gen 1's original release so I had to get the VC versions. Either way, I prefer Blue as a colour to Red

Gen 2: I don't remember but I chose Silver

Gen 3: I got Ruby. I thought Groudon looked really cool at the time.

Gen 4: I got Diamond and I preferred Dialga's design. Diamonds were also really valueable so there is that.

Gen 5: I chose Black and I don't remember why

Gen 6: I chose Pokemon Y because my friend was getting X. I choose Alpha Sapphire because my original Gen 3 game was Ruby.

Overall I think that the box legend has the most influence over which version I choose. For Gen 7 I'm going Moon because Lunala looks amazing.
 
My little sister also plays Pokemon, and she's the collecting type who wants to catch all the important ones she has access to (legendaries, starters, etc), so generally she just convinces me to buy the version opposite of what she's getting so that way she can get both legendaries through trading.
 
Red/Blue
Red, pretty much because of the version exclusives. I have always thought Oddish and Scyther were way cooler than Derpy Plant and Bug That Looks Like A Potato With Horns. Also, it would mildly throw me off if the protagonist was named "BLUE" and the rival "RED".

Gold/Silver
Eh, I chose Gold. I've also always liked Ho-Oh over Lugia, and the Gold spritework is a lot better imo

Ruby/Sapphire
I bet you're sensing a pattern here. I liked Kyogre's design better than Groudon's. Also, my friend sold it to me for $5, so how could I resist that?! Kyogre's still my favorite legendary to this day.

FireRed/LeafGreen
Not really much of a choice here. I got FireRed for a gift (It was my first Pokemon game), but I would've picked LeafGreen. FireRed had Oddish and Scyther, which I do like better than Bellsprout and Pinsir, but LeafGreen had better version-exclusives post-game. Misdreavus > Murkrow. Mantine >>> Qwilfish. Combine that with the lower Porygon price and the mascot being my favorite starter, and I would have chosen that.

Diamond/Pearl
The worst Pokemon main series games imo. Probably never going to get a real copy because Platinum outweighs them both. But I would pick Pearl over Diamond, simply because I like Palkia over Dialga (Not for that reason, you pervs!). Never really cared too much for Steel as a type, despite how good it is (was?), and Spacial Rend is SO MUCH BETTER than Dragon-type Blast Burn.

HeartGold/SoulSilver
Haven't played 'em yet. Probably will sometime after SM comes out. I'll choose HeartGold because I like Ho-oh better than Lugia personally.

Black/White
Pretty much chose Black because I had played Black 2 beforehand and did not really get the plot. Do NOT play Black 2 until you've played Black. It will mess with your head.

Black 2/White 2
I have no preference for Reshiram/Zekrom, but I like Black Kyurem over White Kyurem. I think White 2 is superior, though, because of Solosis, Rufflet, and White Forest (Loved Black City, but I was always a completionist and wanted to catch 'em all)

X/Y
I love bacon as much as the next guy, but X takes the cake, purely because Fairy-type box legendary = awesome

Omega Ruby/Alpha Sapphire
Picked Alpha Sapphire, because I had the original Sapphire and wanted to re-experience the glory of Kyogre and Team Aqua

Sun/Moon
idk really. Leaning more toward Moon, because Lunala seems more creative than Metagross Solgaleo.
 
Gen 1: Yellow because I dislike the Kanto starters and I knew Yellow had better sprites.
Gen 2: Silver because screw Crystal and it's unavailable Mareep. Also Lugia > Oh-Ho by just a little.
Gen 3: Emerald since Rayquaza was (and still is) my favourite legendary ever. he's just such a dope dragon

Bonus:
FR/LG: Fire Red because Leaf Green decided Arcanine was too cool for them.
 
It seems like it's as simple as whichever has most blue cover (X, AS, Moon, soon Sword).
My exception would be Ultra Sun, since I already have Moon and it just fits as I was also just playing Gensou Suikoden V (centering on the Sun Rune), and thus I dubbed the run Ultra Sun Run: Twilight Rune.

It looks like the first game of the region will always be the bluest one, and if there's "third version"/sequel in the same region I'll pick the opposite version.

Oh, also, I play the new games in English first. Japanese later (AS as I've played Emerald, USun, whatever the alternate version of SwSh if I still have enough money for it).
 
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Some of my reasons are really lame.

Red/Blue - I chose red, because I really like growlithe. Seriously that’s the only reason.

Gold/Silver - I chose gold, I am a huge fan of Ho-Oh, and it also had growlithe. (growlithe was my favorite Pokémon before gen 5)

Ruby/Sapphire - I chose sapphire because I got to fight against literal pirates and that’s cool.

FireRed/LeafGreen - Never owned

Diamond/Pearl - Never owned

HG/SS - Same reason as gold and silver

Black and White - Got black version as a gift, I never chose.

Black 2/White 2 - Got white version, since I played black in the original.

X/Y Got X version because xerneas is damn fancy

Sun/Moon - Never owned

Ultra sun/Ultra moon - Got ultra moon because it had better fossils, I love my fossils.

Let’s go Pikachu/Let’s go Eevee - I got Eevee version because my friend got Pikachu. Wish it was the other way around though because Pikachu version has growlithe.
 
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Generally, I've been lucky since me and my twin could get a different version each and trade as we see fit.

Red/Blue: I picked Blue because my younger self really liked Blastoise.
Gold/Silver: We had Gold before Silver as we got a ton of GB games in a job lot. When we got both though, I still picked Gold because I liked it more as a color.
Ruby/Sapphire: See Blue but replace Blastoise with Groudon.
FireRed/LeafGreen: My brother really liked Charizard at the time so I picked LeafGreen. I know they aren't version exclusives but hush.
Diamond/Pearl: See Blue and Ruby but replace Blastoise and Groudon with Palkia.
HeartGold/SoulSilver: I had Gold, so decided to keep things consistent and picked HeartGold.
Black/White: My brother wanted to use a Lilligant with Own Tempo, so I picked Black.
Black 2/White 2: I picked Black 2 to keep the story consistent; I also wanted that Shiny Gible dammit!
X/Y: I chose X so that I could use Starmie.
OmegaRuby/AlphaSapphire: Primal Groudon's typing and ability seemed so fun that I picked Omega Ruby.
Sun/Moon: I wanted a Vulpix, so I bought Sun.
Ultra Sun/Ultra Moon: See above.
 

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