>>51173784always pick the third version it simply has more stuff and doesn't really remove anything, same goes for Ruby/Sapphire/Emerald and Diamond/Pearl/Platinum
UNLESS
the third version is missing pokemon you want to use.
>>51173431first post, best post.
The thunder-giraffe Ampharos is quite popular, so that's really all there is to it when it comes to picking a version.
>>51174202a pokemon being bad, just means it needs a few more level-ups. I used Chikorita on my first playthrough and didn't have a problem.