I thought I'd clarify exactly why some people didn't like the Gen III designs or games too much. If you started with the Gen III games, it's just a tiny bit hard to understand.
First thing's first - the designs. Although some people really don't see the difference between 1-251 and 252-493, there is, off the bat, one thing that sticks out to me:
A fair amount of the Gen III Pokemon look like Digimon. I like Digimon, but when Pokemon started copying it, a little bit of both franchises died.
Cases in point: Combusken, Beldum, and the overall amount of black around the eyes on the Gen III legendaries. Who can look at how Rayquaza's eyes are shaded and NOT think 'Renamon?' Moreover, the designs got increasingly mechanical, and almost too simplistic compared to the previous generations. Go on, tell me that Latias looks like a plausible organism.
Second, Team Aqua and Magma are double-edged swords. Yes, they are more terrorists than petty criminals (like Team Rocket), but they also started the trend of "organization has big plans, then bites off more than it can chew." You'd think that, if they were more competent than Team Rocket, they would have been more prepared to handle a giant crayfish with hugeass claws (or, in the case of Kyogre, an orca whale with prominent digits). It's a bit annoying that the organizations from Gen III on lead you directly to the legendaries. Gen IV is extra guilty of this.
I suppose it's kind of like what happened to artists like Shakira and Jewel: they did what they wanted for a few albums, then suddenly changed style. Compare "She Wolf" with Shakira's earlier stuff; the analogy is so similar it's really kinda scary. Hooray for mainstream compliance?