I also have to wonder: What is Gamefreak's main goal when making Pokemon games?
This is an interesting question that I think everyone should wonder before they take sides on this argument. This would tell us where the priorities are and how they release games. For me, it seems that, with the exception of the 5th and 6th generation (which I'll get to in a bit) they were focused entirely on the Pokemon themselves. It felt like the world around them were developed as an afterthought.
It seemed that way especially with the 3rd generation. Ruby and Sapphire weren't compatible with the previous games so you couldn't catch them all. So, we had Colosseum and XD come out to help fill the gaps. Then FireRed and LeafGreen came out to both celebrate the 10th anniversary of Pokemon, but, for me and many others, it existed to give us a chance to catch the missing Pokemon. Finally, Emerald came out. Emerald was the polished version of Ruby and Sapphire. Now that they had more time for development, they had more time to actually develop both the world (giving us the expanded story) and add extras to satisfy the loyal fans (e.g. the Battle Frontier)
In the 4th generation, they were experimenting with trying to bring the Pokemon as part of the internal story and structure of the region. You have to admit in the 3rd gen, the legendaries just seemed to exist in those areas and, for the most part, they didn't really NEED to exist in the region when other made-up areas would suit it just well. You can't say the same about the LAKE trio or how PokeGods wouldn't prefer to live on top of a giant magnetic mountain. Of course, they made the game have a lot of bonuses to those that had previous versions (like all the new evolutions). Platinum was similar to Emerald. They already built the games and now they had time to polish them, add back the features they removed because they didn't have time to make them perfect (With the changing mechanics it would have been disastrous just to port all of the Battle Frontier from Emerald to Diamond and Pearl without changing anything) as well as fix common complaints (like not enough Pokemon in the dex for Gym Leaders and Elite Four members to even use!). HeartGold and SoulSilver felt like a step forward because they changed a few more things, but it honestly felt more like an updated nostalgia game than FireRed and LeafGreen. They changed things that made use of the new features they added as opposed to those two. Plus they fixed and extended the sparse Kanto (though they didn't add a lot of new content there). I KNOW many of us bitched at the copy and paste Battle Frontier but, hey, it's something! They could have made new leaders though...
The fifth generation was the one generation I felt they slacked off on the mon-building. Instead they focused on telling a story in a region way different than the previous ones and that's why it was located far away without any of the old Pokemon in it. Of course, whether you like the story or not is not my concern right now, but you have to admit there WAS a whole "Story is top priority" feel for Gen V. In fact even the main legendaries (Reshiram and Zekrom) felt like they were in a supporting role to the story. They didn't NEED to be Reshiram or Zekrom for the story to make sense unlike Kyogre, Groudon, Rayquaza, Dialga, Palkia, or Giratina controlling their forces. In fact the whole Truth vs. Ideals things didn't make much sense considering the alternate version was Ideals vs. Truth and that it was just N grabbing one orb and giving you the other. B2W2 again had more time to change stuff. Unlike the others, a radical change was made to like make a whole new Unova filled with old Pokemon (thanks Poke Transfer Lab). Since most of the work was already done again, they had time for world building and polishing giving us the whole PWT and PokeStar Studios.
Gen VI was the oddball to me and I seem to get
Codraroll's complaints here the most compared to other generations, but I'm going to try to play Giratina's advocate here. It seems like they decided to go right back to the basics. It felt that they wanted to invoke a sense of nostalgia to the first generation without re-releasing it. It also felt like they also wanted to world-build in terms of making a world where Mega Evolution actually makes sense. I can see them running out of time and not having enough time to make new content much more beyond what they had. They released the games pretty quickly after B2W2 and they had to make the entire game make sense in 7 languages simultaneous to have a single world release compared to all the previous games. This generation felt like this was the one generation MADE for competitive battle (though it felt like they failed with the whole existence of Mega Kangaskhan). ORAS was released on even less time. It honestly felt like all they really had time for was updating graphics and making a Mega-Evolution capable remake while keeping the rest constant. This was one of the quickest turn arounds for a game that I ever really saw. I was barely done with getting tired of XY when ORAS came out. I don't think they HAD time for redoing the Battle Frontier. To be honest, just copying and pasting the XY Battle Maison to ORAS was the point that I know EVERYONE hated. Ok, I could have dealt with the Battle Maison (I would have preferred a Battle Tower like in the original RS but I could live), but the main problem is having the EXACT SAME leaders as before. It would have been interesting to say that they built a temporary thing based off of what Kalos had and they staffed it with a bunch of random people while the Battle Frontier plans came together, but this is just lazy. The only excuse I can allow is just how quickly they went from XY to ORAS. Maybe they had plans for new Megas they didn't have time to flesh out in XY so they remade RS and put those Megas in and finished up the rest of the RS starters and legends? idk. Maybe hearing the fan's disappointment in the features of ORAS cause Gamefreak to postpone Pokemon Z until they finally added all the features we were clamoring for? If they do, I'm certain it'll restore MY faith in Pokemon... I guess we won't know for sure until it comes out!