I just remember a lot of people at the time of release not being happy with the fact that none of the previous four or five hundred Pokemon would be featured in the game, of course they fixed that up with Black and White 2. Personally, they are my least favourite games in the main series so far. Probably a bit harsh to say if anything was going to kill off the Pokemon game it would be that generation, but I do believe it was the closest anything has come to this point, even if the series was still for from dead.
I thought you were referring to the limited time-span. I believe it had the shortest time-span of any generation in the series, lasting only two years compared to the average three. Plus, it was the first generation not to include a console tie-in game and remake iteration. Plus releasing it on the Nintendo DS made it feel less significant compared to other generations (only Gold and Silver share that distinction and it wasn't promoted as a series revival).
I remember those complaints, but I don't recall it being as prominent. I suppose when you're on that side of the fence, it can seem that way, but I remember it being more hardcore friendly. The generation seemed to pander more to the veterans of the series who were sick of battling Zubats, Geodudes etc. all the time and wanted a change of pace.
I can't really speak on behalf a bunch of communities because it varies from place to place. So speaking from my own experience, I remember enjoying the more thematically rich story, the US inspired location, the way HM puzzles were implemented and the reusable TMs. A lot of the new monsters were fun to use and they finally made some use of some items (why wasn't Lucky Egg a staple from Generation II?!).
Then the sequels came along and from the outset announced themselves as the best Yellow, Crystal, Emerald etc. version of the lot. New story, new locations, more monsters, more post-game, more side-quests, new gyms etc. It was fun and it seemed to be a lot more challenging. The only downside was the implementation of hard mode and how counter-intuitive that was.
As far as what could kill the series - Gen III faced some tough challenges. It hit the reset switch on the entire series, on one of the least successful handheld systems, after the series had worn out it's welcome as a fad. A lot of people clocked out around this time, but it found it's new audience and was able to grow from there.
Low point personally is Diamond and Pearl. I enjoyed them initially but when I went back to play them before Black and White, I realised how slow and cumbersome everything felt. Performance wise, there seemed to be a lag to everything the game had to offer and the adventure itself was forgettable with a lot of monsters hidden away until late in the game. It's a shame because online, the physical/special split and DS features made the games so good but the system couldn't handle them. Heart Gold/Soul Silver and Platinum redeemed the generation.
