In light of the above posts, how's this for unpopular, then?
There has yet to be a "really great" Pokémon game.
I mean, I really like the Pokémon games, but they've all had some pretty glaring deficiencies that's hard to overlook, and somewhat easy to address.
Gen I was the prototype, and listing its deficiencies would take too long and not be practical. One word, for brevity's sake: Postgame.
In Gen II, the famous level curve is all that needs to be mentioned. Again, trying to keep things brief. Also, Johto is a remarkably bland region.
RSE were very pretty games, but the Pokémon selection in those games had issues. Also, whoever coded those sea routes and thought Tentacool, Wingull and Pelipper were enough Pokémon to fill out the wild battles needs to be smacked. RSE also had it pretty bad in terms of post-game Pokémon levelling. Emerald arguably had the best post-game facility ever, though, and Secret Bases were pretty fun too.
FRLG suffered from many of the same problems as RBY, although the postgame was greatly improved, and the VS Seeker alone added heaps of content. Still, obtaining all Pokémon was a bit of a chore, especially considering the tedious sidequest you had to go through to unlock the rather basic feature of trading with the RSE games, effectively preventing you from using nearly two thirds of the Pokémon available at the time for a playthrough.
DPPt presented us with an amazingly bland region, a rather limited Pokémon selection (a whooping two families of Fire-type Pokémon aside from Chimchar) and a tediously slow battle engine. The games deserve credit for introducing the physical/special split, and making a bunch of Kanto and Johto Pokémon a lot more interesting and relevant, but they had their massive faults too. And HM usage this gen was frankly ridiculous. It was impossible to go anywhere without bringing multiple HM slaves. And the return of the Secret Base system was so half-assed they might as well not have bothered with it.
HGSS, like their predecessor games FRLG, retained many of the problems of the original games. The level curve in Johto is barely better than it used to be, and the battle engine is only marginally faster than DP's. Still, I feel HGSS is one of the better Pokémon games out there, for its time. It made many of the right choices, and few outright bad ones.
BW decided to "start anew" with only new Pokémon to play with - and then made half of them conceptually identical to old Pokémon anyway. Trainer rebattles got axed, the game is extremely linear, and all roadblocks are variants of "do this specific task to gain access to the next area". Also, the elemental monkeys. The lack of a Battle Frontier was also disappointing. Still, it deserves great kudos for some design choices such as multi-use TMs, respawning Legendaries, dynamic background music, the addition of Hidden Abilities and engaging multiplayer minigames. The gradual deterioration of White Forest and Black City was a bad idea, though. One thing is needing to play with people to bring the population up, but lowering it back down automatically as time goes by? Meh.
BW2 are another highlight, and in my opinion the best Pokémon games yet. All the good things of BW1, but with most of the bad things removed. It did not bring back the acclaimed Battle Frontier of previous generations, but between Join Avenue, the PWT, Hidden Hollows and Black Tower/White Treehollow, it's almost excusable that they simply copied BW1's Battle Subway. BW2 were interesting to play through, and interesting to continue to play long after you beat them.
XY did some things really well (the Kalos region looks amazing, the music is great and the Pokémon roster unparallelled), and some things... not so much. The story is generic and bland, there is no long-term postgame outside the Battle Maison, Elite Four rematches were removed for no reason, as were Gym Leader rematches, dynamic background music is no more, and the postgame areas are restricted to one city. At least the Restaurants and Battle Chateau made Pokémon training really convenient. And of course, we only ever saw one iteration of Kalos, despite amazing potential for a sequel.
ORAS decided to roll with many of the problems of Ruby and Sapphire, without implementing the fixes from Emerald. The post-game battle facility was copied over wholesale from XY - down to the last detail, name and everything. The DexNav was the most amazing and convenient implementation of the Pokédex ever, though, and the QR code system for sharing Secret Bases a genius move. But ORAS lacked overall staying power, with a weak long-term postgame, and Hoenn's most-anticipated and best-loved feature absent in the most trolly fashion ever. And although most legendary Pokémon from previous generations are available, they seem to be thrown in without consideration for whether it makes sense or not.
SM are, in my opinion, the best-looking Pokémon games to date, but also a conga line of terrible design choices. There is no postgame to speak of. Wild Pokémon encounter tables are insulting, you meet the same handful of Pokémon everywhere, while roughly half of all new Pokémon are unnecessarily hard to find. Triple Battles are removed, and the few Double Battles there are, are amazingly laggy. The most exciting feature of the previous generation is blatantly sidelined in order to promote The Next Big Thing. Training Pokémon is the slowest it has been since RSE, with no good training spots and no repeatable Trainer battles save for the Elite Four. Multiplayer is turned into a chore with Festival Plaza. And DexNav, the most amazing feature ever invented in a Pokémon game? Totally scrapped. Instead, your Pokédex is cracking jokes.
Every game seems to have some flaw that deteriorates the game experience, a sort of "what were they thinking" moment of bad decisions. It's almost as if I'm suspecting that Game Freak intentionally put flaws into their games, so the next game will look better by comparison when it comes out. They never set the bar so high that it becomes difficult to jump over the next time.
