So I just got a 3ds, and since there aren't too many games out for it quite yet, I thought about trying to get into Pokemon. The thing is I'm a completionist / crazy person and if I start down this path, I want to be able to collect as many of these guys as I can as a long term goal. I did some research this weekend and found out you start with the generation 3 games for GBA, then you can transfer those between each other and then onto generation 4, and then from 4 to 5, which is the latest one.

My main question is once I go through the GBA games, which are cheap enough so I don't really mind getting all 5, would I have to get every version of the DS games? Or does the games' online trading capabilities alleviate that need, such that I could just get, for example, Platinum, Soulsilver, and White, and be able to fill in the gaps? I have enough old Nintendo equipment that I could do my own trades but I don't know anyone else that plays locally. If I could save myself a little time and money if some of the games are identical except for exclusive Pokemon, I'll do that. If the games themselves are different enough though, I'll play through them all. Like I said, it's a long term goal.

Question 2, how hard is it to find the limited special event Pokemon on the online trading system? I'm not too concerned with those if they're too rare, but it seems like Nintendo adds ways to get older ones every so often.

Lastly, what's the best order to play through the DS games? I know probably for GBA you play Fire/Leaf, then Ruby/Sapphire, then Emerald, but I'm a little lost after that. Thanks.

There is a system called the Global Trade System. You can put a pokemon up for trade or search through pokemon others have submitted. If you are putting up your own pokemon for trade, you select which pokemon you want in return and any other specifics such as level range and gender. However you need to have seen the pokemon that you wish to trade for, or you can't select it. Searching for individual pokemon this way is annoying, as most people ask for legendaries or super rare pokemon in return, but if you deposit your own for a fair trade you'll get it in a short time.
 
You can also add someone with a friend code and manually trade with them. Head over to the gamefaqs trading boards or serebii to find some people to trade with.
 
If I remember right lots of special event pokemon have ribbons that prevent them from being traded to others.
 
Best order would probably be Diamond/Pearl/Platinum, Gold/SIlver and then Black/White. Which is the order they came out in.

Thanks for the reply. I gotta say though I wish I would have gotten into this about 2 years ago when Gamestop still had used GBA games. I've had to educate myself through youtube on identifying counterfeits, and still my first shipment arriving today turned out to be one, really convincing too. Hopefully I'll have better luck tomorrow, as well as hassle free return.