In the main pokemon games, Pokemon are put in the pokedex by generation. But sometimes... they decide to make a new evo for a pokemon, and put it far away, in another generation.

#41 Zubat - #42 Golbat -> #169 Crobat
There's 126 Pokemon between Golbat and Crobat.

By reorganizing the pokedex, we could be able to put Crobat beside Golbat, and many others, like Sneasel and Weavile, happiny and Chansey, etc.

And since the 6th Gen is coming... do you think it's a good idea?

As long as they do it correctly, and try to stick to certain guidelines.
Gen II's dex was a heart attack until I learned how to revert it back to original order.

Wow.... it's a mess o_O
No logical order at all... but at least Crobat is beside Golbat!

Maybe for the Kalos regional dex we'll have another jumbled up pokedex listing, with (just a possible example) the Elekid line all together and Zangoose ahead of Farfetch'D. I think for the national pokedex they'll stick with the original format with Pichu being way behind Pikachu and Raichu as always, along with the other possible examples. Or maybe they'll edit it, who knows? However the way it is is obviously designed to distinguish the generations.

No.

Regional Pokedex scrambles are already stupid. Keep it the way it is; it sorts Pokemon based on what Gen they were introduced. Unova's was the only one I could really bear because it was in the same order as the National Dex, AND in the same order they appeared in the game. All the others (Kanto excluded for obvious reasons) were hellish to deal with.

I already deal with enough stupidity with this "[region] Pokedex" nonsense. There is no need to know the number of a Pokemon in more than 1 Pokedex. The National Pokedex must remain a static unchanging standard to be able to refer back to.

Because then Bellossom becomes #51 and everything after that just gets weirder.

While I'm not against the idea, I don't think that the Pokédex needs to be reorganised, and I don't think it ever will.
What may happen is a new Pokédex function that sorts Pokémon by type and Evolution line.

What about Normal/Flying and Dragon/Flying. Altaria wouldn't belong in the Normal Category, even though it evolves from a Pokemon with Normal as its primary type.

But that goes against the idea of using their primary types.
They could just change it so that they're Flying/Normal and Flying/Dragon, and then they'd fit in the Flying Category.

I think that in the next pokemon games the national pokedex should be reorganized. Mainly because I think that all pokemon that evolve should have their evolutions right next to each other. For examaple
Magby's evolutions are all over the place. Magamar is in the 1st gen, Magby's in the 2nd gen. and Magmortar is in the 4th gen. I just think it would be a lot easier to navigate through if everyones evolution were right next to each other.

oviously as the pokemon evolutions are scattered