The new Pokémon games are good. You should play them, if you can! The question is, which game should you pick up?
Pokémon is unique in that, if you want to play it, you always have a choice between two different versions of the same game. Typically, the versions are denoted by colors or stones—Red and Blue, Black and White, and so on. Traditionally, each version has creatures that the other version doesn't. This encourages people to play with friends, since that's an easy way to swap version-exclusive Pokémon.
The first thing to consider might seem silly, but it really is important: which color do you like better? I'm partial to Red colors, so that's why I went with Ruby.
Right now, as far as I can tell after comparing notes with people who have played Sapphire, both versions of the game have the same mega stones—those items that let select Pokémon undergo a special stat-boosting transformation. That is to say, there are no version-specific mega stones. I've even found stones for each of the two versions of the same Pokémon—like both Mewtwonite X and Mewtwonite Y in my copy of Ruby. Even so, you'll still have to do the work to find the stones, of course, and for that I'll direct you to my tips piece which drops later today.
Beyond that, the major differences in versions have to do with Pokémon. As far as I can tell, the differences are the exact same as they are in the original games, plus a few additions. So, to give you a list of Pokémon:
Ruby: Seedot, Nuzleaf, Shiftry, Mawile, Zangoose, Solrock, Ho-Oh, Palkia, Tornadus, Reshiram, Skrelp, Dragalge.
Sapphire: Lotad, Lombre, Ludicolo, Sableeye, Seviper, Lunatone, Lugia, Dialga, Thundurus, Zekrom.
Fun fact: some of these Pokémon have the sort of lore that supports the rivalry that comes with having two versions of Pokémon. You may not know this, but there is totally some tribalism and pride that comes with picking a version! And so it may not surprise you to hear that certain Pokémon that I just listed have rivalries with each other, too. Zangoose and Seviper are said to be in an eternal feud, according to pretty much every Pokedex entry on them.
Personally, though, I think Ruby's Zangoose, pictured below....
...looks a hell of a lot cooler than Sapphire's Seviper, pictured below:
But that might just be me. You can make up your mind here, obviously. Going back to what I was saying before, another pair of Pokémon that riff on the two versions thing are Lunatone and Solrock. They're shaped like a moon and a sun, respectively.
Legendary-wise, you have two major considerations. If you pick up Omega Ruby, you get Groudon (pictured on the left), along with Groudon's primal reversion form (pictured on the right):
Normal Groudon is a Ground Pokémon, as the name suggests. It has the "Drought" ability, and it can expand the landmass. Groudon also has a special ground-type move that only it can learn, Precipice Blade. When it changes into Primal Groudon, it becomes both Ground/Fire type, gains the "Desolate Land" ability—which makes the sunlight turn harsh. Mechanically what this means is that moves like Rain Dance, Sunny Day, Sandstorm and Hail won't work, nor will abilities like Drizzle, Drought, Sand Streak and Snow Warning. Really, in general, water moves—the thing that Groudon would normally be weak to—become ineffective against Primal Groudon.
Groudon appears in Ruby because of Team Magma, pictured on the left here:
If you pick up Ruby, Team Magma will be the major villain you have to deal with. What's their evil plan? Well, they want to increase the landmass. That's where Groudon comes in. Team Magma foolishly believe that more land will somehow enable humanity to make more progress, completely ignoring the fact that water is kind of more important than land. But they wouldn't really be a super villain if they were sensible, now would they?
On the other side is Team Aqua. Frankly, Team Aqua is the more charming team. They're pirates, for crying out loud! Their leader, Archie, seems like a cool guy to hang out with. You know, aside from the whole "wants to increase the size of the ocean" thing, which is Alpha Sapphire's plot, should you pick that one up. But it's easier to be empathetic with this ridiculous plan, since Archie wants to bring back the Pokémon habitats destroyed by humanity. I can almost get onboard with that.
In any case, Team Aqua plans to achieve this goal with the help of Kyogre, the legendary Pokémon you can capture in Alpha Sapphire. Kyogre, pictured on the left, can turn into Primal Kyogre, pictured on the right:
Kyogre is a water type Pokémon that has the ability "Drizzle." It can learn the move Origin Pulse, as well as transform into Primal Kyogre. Once it does, Primal Kyogre's special attack becomes boosted, and it gains a special ability called "Primordial Sea." This ability makes the battle come under a heavy rain, and this heavy rain makes moves like Rain Dance, Sunny Day and Sand Stream, as well as abilities such as Drizzle, Drought, Sand Stream, and Snow Warning all fail. As you might expect, all of this means that fire moves can't do diddly squat against Kyogre.
The other two legendaries you have to take into consideration are Latias (pictured on the left) and Latios (pictured on the right).
For these Pokémon, you'll get the color opposite the version you pick. So if you get Ruby, you'll have Latios, the blue one. If you get Sapphire, you'll get Latias, the red one. These Pokémon can mega evolve, as you can see in this trailer:
I'd say choosing between Latias and Latios is more important than choosing between Groudon and Kyogre. That's because Latias and Latios are the Pokémon you'll get a chance to fly around Hoenn, like so:
So pick wisely!
And there you have it. Those are the big differences between Omega Ruby and Alpha Sapphire, as far as we know right now. The two other big legendaries, Rayquaza (on the left) and Deoxys (on the right), will be available on both versions, so don't worry about that.
It's worth noting that this article doesn't list the version-exclusive legendaries you find while using the Eon Flute, because there's just not enough information floating around about what Pokémon are in which game yet. We'll update this article as soon as we know. For now all we can say is, regardless of which version you pick up, you're going to have more legendaries than you know what to do with, because it's possible to collect every legendary in the franchise thus far between both versions.
Finally, I'll note that while it's easy to criticize the whole "two versions" thing as just a business move, meant to sell more copies of what is essentially the same game, I actually found some merit to the idea while playing through ORAS. I played Pokémon alongside a friend this time around. She played Alpha Sapphire, while I played through Omega Ruby. We both started at the same time, with the goal of beating it around the same time frame. Let me tell you, it changed the experience completely. Having someone to compare notes with, trade Pokémon with while you sit next to them making jokes made playing Pokémon way better. We'd do things like catch Pokémon with the explicit purpose of gifting them to each other, we'd trade Pokémon with jokey names, and we helped each other find hidden mega stones. We also helped each other with the Pokémon that our versions lacked, meaning it was easier to fill up our Pokedex. So if you have the ability to do it, I suggest that whatever version you pick up, you try to get a friend to pick up the other version with you.
I'm curious: what version are you thinking of picking up? Complete speculation over here, but I'm guessing that Ruby will be the slightly more popular game. There's always one version that slightly outsells the other version, at least. We'll see what happens, though!