IMO the best designed agents are the ones who have abilities with good synergy so they are well thought out and not just good in game. for example, omen deafen + tp, smoke + tp, i think those were a smart combination of abilities and makes him extremely fun to play. cypher with his x-ray from his tripwire and ultimate and camera + smoke. fade's abilities make it easier for her prowlers to catch a target. there's still more like sova, killjoy, deadlock, raze, viper, even chamber and loosely iso and sage.
if i had to pick one between the best it would probably be jett because her entire kit seems well thought out and very fluid. the abilities still find value without being used in combination with others but they are made even stronger when used together. :)
there are a few standout agents who seemingly (to me) have abilities with almost no connection to each other outside of lore. characters such as harbor and clove just seem to me like they had a bunch of junk for ideas and abilities selected out of the junk. i understand that they may be good in game but none of their abilities really meld like the others so between them would be my answer for worst designed.