Objectively speaking, I'd say the best Pokemon design might be something like Nidoking or Nidoqueen. Part of what makes them awesome is that they're not a dog, not a snake, not even a mammal or a reptile but just Nidoking and Nidoqueen, plain and simple, and yet the mammalian and reptilian traits blend so smoothly and naturally that they don't come off as being at all awkward or creepy. The evolutionary transitions are neither ridiculous nor insubstantial, with a larger jump upon undergoing the stone evolution into their final form,the level of complexity in the design is just about right the male/female difference is reasonably believable, the typing of the final forms remains unique and interesting, and the whole thing just feels right.
On the other hand, Generation I had some pretty stupid designs as well (most of the problem stems from the fact that several Pokemon are almost - if not entirely - identical to real-world animals. Granted, this has hardly stopped being the case, but just look at Krabby, for example. That thing's worse than Basculin!), and a lot of my favorites, including Torterra, Flygon, Reuniclus, and the grand-mother-of-all-things-awesome, Golurk, come from more recent games. Honestly, I think Generation 2 is something of an oddball, as it has (in my opinion) the fewest absolutely despicable AND the fewest mind-blowingly amazing designs. There are still a fair few that are pretty cool, though, like Dunsparce, Tyranitar, Scizor, and Steelix, and Meganium wins the non-existent award for cutest fully-evolved starter.