If we're not excluding flying Pokemon, then probably Yanma. Dragonflies are known for being extremely agile and fast for their size, and Yanma is a giant dragonfly. Yanmega, on the other hand, looks a lot bulkier and slower (this is even evidenced in its stats by its Speed not being particularly high, whereas Yanma's Speed is its best stat).
For grounded Pokemon, probably Grovyle. Maybe it's that its sprites usually depicted it mid-sprint or mid-leap or maybe that it's partially inspired by the popular Western depiction of a ninja, but something about the entire Treecko line, especially Grovyle, makes them seem exceptionally agile compared to other Pokemon.