What about FRLG and HGSS? Did you not pick them up?
I usually skipped the third version/remake since the third version was usually just an enhanced version of the pair games and being I played the originals games I never felt I needed to get the remakes which was for the most part the region with updated graphics and mechanics (yes they added stuff, but for some reason the added stuf never drew me in). Of course as of recently things started to change. For BW2 it wasn't an enhanced version of the pair games but rather a sequel with an entirely new story that continued from the previous one. As for ORAS the introduction of Mega Evolution and moving onto 3D graphics made me think they were going to change up the story and locations. And while they did, it wasn't to the extent I thought they were but I still enjoyed it (also it having all the new Mega Evolutions convinced me to get it. I was also hoping it would have the Battle Frontier but obviously that fell through). That said my brother did get Yellow and Crystal, however he fell out of the Pokemon fad. Also I watched playthroughs of Emerald, FRLG, Platinum, and HGSS so I know what changes they did in those games.
Sorry for double-posting, but I just realized I forgot something:
I also have one question in particular - do you think there is a bias in that people tend to pick the "leading version" more often? By leading version I mean, Red, Gold, Ruby, Diamond, Black, X and so on.
I think most of the time the determining factor is the Pokemon on the box since it's at least known by everyone that you get that Pokemon but not the other one (usually). Let's go by generation:
Gen I: Red & Blue
While a turtle with cannons sticking out of its shell probably appealed to the hardcore kids (or the title's color was the player's favorite color), for most everyone else I think a dragon probably drew in more purchases. I'd argue in Japan where the choice was
Red & Green the same rule applied: dragon over flower frog.
Gen II: Gold & Silver
Unfortunately for Ho-Oh, Lugia just starred in the most recent Pokemon movie. I guess Ho-Oh did have the most valuable metal as its game title, but I would think Lugia was on a lot of players' mind due to the movie.
Gen III: Ruby & Sapphire
Hulking dinosaur beast vs. odd big-finned fish. Though like with Gen I favorite color would play a role.
Gen I-R: FireRed & LeafGreen
As I said above, dragon vs. flower frog. Though once again favorite color could play a part.
Gen IV: Diamond & Pearl
Dialga had a bit more of the fiercer design (not being pink probably helped with that) and diamond is a more valuable and harder gem than a pearl. However I could understand those who didn't like Dialga being a quadruped dinosaur and preferred the more dragon-like Palkia despite being pink.
Gen II-R: HeartGold & SoulSilver
Hmm, hard call. No movie bolstering one of them so I would say Ho-Oh probably had the better chance here because of the gold in the name. However the "heart" part could have driven away some to SoulSilver since "soul" is a gender-neutral thing. I suppose you could also say Lugia looks a bit more dragon-like, but I don't think its enough to balance the scale in favor of the more obvious phoenix-based Ho-Oh.
Gen V: Black & White
A graceful white angel-bird vs. black mecha dragon. I don't think color played a role unless you wanted to go with a race joke.
Gen V2: Black 2 & White 2
I actually imagine this was more driven by what first Gen V you got. But if you didn't get those then I think MAYBE Kyurem Black would attract more simply since it incorporates themes from the previous popular black mecha dragon.
Gen VI: X & Y
Death vulture vs. life deer. Color could also play a part and maybe even gender if a player knows a person's gender is based on the 23rd chromosome.
Gen III-R: Omega Ruby & Alpha Sapphire
The hulking dinosaur beast is now covered in magma while the odd big-finned fish only got some transparent skin.
But as we've discussed everyone has their own reason and from what I'm reading its just as often getting the opposite version of a friend/sibling then for choosing due to color/Pokemon on the box/or whatever other reason.
Tl;dr: No, I don't think a version being "first" or "second" have anything to do with it. Infact I'm sure a lot of players don't even see it that way as that sort of makes the false connotation that one version is superior over the other.