So you think that a change in developers doesn't lead to a change in the name and in it's features.
No. Again, names are largely meaningless. The change in naming scheme and the addition and later subtraction of the "story mode" were a function of development decisions, not a change in developers.
never mind that they tried to make the obvious connection with the name Pokémon Colosseum
And the connection you think they made was...?
but i think you cannot say that releasing a game that is supposed increase the battle experience without 3D when the portable games have it is a good idea (especially after how Pokémon Battle Revolution did).
First and foremost, you've managed to confuse definitions of 3D.
PBR - and any console game - is claimed to have "3D" graphics because all of the involved onscreen graphics are built from polygons rather than sprites. Being composed of polygons gives the game's models depth - the models can appear to move in any direction, including "towards" and "away" from the viewer - height, shadows and everything else associated with an actual "real" image. The punchline is that the image is still created and displayed in two dimensions - the image is not designed to fool your brain into seeing actual physical depth or seeing it "leave" the confines of the display.
On the other side, the 3DS is capable of displaying in what's called autostereoscopic 3D, which is the technology of displaying two identical images that are slightly offset from one another, a process designed to fool your brain into fusing the two images into a single super-image with actual depth when it processes the two images together as one. Look at the image output by the 3DS and you will experience the illusion of seing an actual physical image with depth, appearing to extend "deeper" into the display and appearing to move "towards" you.
With all of that said, the 3DS is not a Nintendo console: what it can do visually has no bearing on anything in this discussion. And to further that, Pokémon is not a visually-heavy franchise even when it is on a console. What is it you think "3D" would really add to the "battle experience"? Water and fire "coming out of your screen!"? That's gimmicky. They wisely avoided doing something like instituting motion controls with PBR that required you to "throw your Wii Remote!" to "throw" a Pokéball or anything like that; let's leave the gimmicks to developers who have nothing worthwhile to contribute.
Again, what the 3DS can do is completely irrelevant to the discussion, as is most any Nintendo handheld, given that the entire point of the console battling titles is that they give gamers an opportunity to battle their Pokémon in 3D - that's polygonal model 3D, not autostereoscopic 3D - on their televisions rather than their handhelds. That's not a function they will ever move to the handhelds, because it removes the console benefits from the equation and because a completely polygonal game, Pokémon and all, is still too resource-intensive for even a stronger handheld like the 3DS.