This is like if Bioware released 2 versions for Mass Effect, one with Paragon path and the other with Renegade path. 

Its stupid and it doesn't make sense.

So I'm assuming this game is available on the old 3DS? just for future reference, how can I tell if the game is available on both or not?

Edit: it says so on the cover.

I doubt it that's gonna be a huge fuck you to the Japanese gamers.  There's no way my SD card on my 3DS is gonna hold a full game, so even if it is a reduced price it doesn't really matter to me because I have to buy a SD card to even play it so that's gonna be another $10-15.

No! Is different! JAPAN will have two differents games that will culminate in some point, while the rest of the world will get the two stories in just one game

Nowhere near comparable.

1. Its most likely only japan (they done this beforewith games).

2. The Price is equivalent to $45 but with the other game as DLC its $15. Total is $60. 

3. They aren't exact copies off each other, you can literally say they both are completely different games.

4. Lots of HH games in Japan go for ¥6000-¥7000 anyway, especially JRPGs.

5. It might cost us in the West $40 or even $50 which is well worth the price (comes with both games)

Please tell me.

The other side is NOT DLC for the west.

That's not quite the right analogy. It'd be more like Sacred Stones came with two versions: Ephraim's route and Eirika's route, even it the two met up in the end. I'm unpleasantly surprised that Nintendo is doing this...

and people complain about MSony's dlc practises...

It is an Oracle of Ages/Oracle of Seasons type of thing. That's ok, especially since the total price isn't $80, but probably something like $50-$55, which is like the cost of a 3DS RPG + DLC.

It would likely cost less than a Sony/MS dlc + full game, and you get more content.