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The Pokemon designs were admittedly very hit or miss, but gen V was the peak of the series mechanically.
Constantly animated sprites, while blotchy, had more actual personality than the flat sprites or 3D models ever did. Its the first and only time they ever dabbled with the idea of a hard mode, even if it was implemented poorly. The story, while silly and campy, was probably the most in-depth and well written is had ever been, much better than VI. Its also the first and only time they have ever tried doing a legitimate, real sequel to a Pokemon game. Even without the challenge mode the pacing of the game was pretty good. It had a plethora of interesting and fun side missions and activities. BW2 are the kings of postgame. The rivals were friendly without being mindless like in VI or VII, and they weren't jerks like in I or II; they had goals and stories of their own. Most of the side characters are memorable, some of my personal favorite gym leaders come from these games. A lot of the region is also very memorable, and they were ambitious with the scenes and camera shots they tried using.
Although I can't say gen V is my favorite, I have to admit it honestly was probably the best the series is ever going to get.