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I can see and understand the reason for the controversy, by sheer new content gen 2 was a tough act to follow and though abilities and natures were a great introduction they weren't a pair of new types. By the same token, this was the first time where the franchise showed that it had somewhat stagnated and wouldn't be budging from the basic formula that was around since gen 1, gen 2 at least had neat surprises like going back to Kanto and facing Red, but gen 3 didn't really have anything like that.
That said, gen 3 still has the fastest, most smooth battle speed and a lot of the pokemon introduced were neat. I just don't remember it as fondly as I do gen 2, and I was still a young kid when I first played Ruby.