Generation 2 brought us great new Pokemon, and the Johto region showed us that even though the region is small, it can be filled with great Pokemon and locations. From the new Steel-types such as Skarmory and Scizor to the Legendary Dogs and Birds, to the Starters, everything about Johto is great.
Generation 3 is close behind, as it gave us the only good "fresh start" in the series. While Generation 5 certainly gave us a fresh start, the Pokemon were covered with pointless patterns and didn't have much of a Pokemon vibe. However, Generation 3 gave us a great fresh start with extremely exotic-looking Pokemon. However, these exotic Pokemon still had that Pokemon vibe, and there was a good reason for the Pokemon to look exotic: Hoenn is a tropical region. Even in real life, the animals in tropical areas look much different. So, for those reasons, Hoenn is also a great region.