The only bit of advice I can come up with at the moment is turning Jonathon into one of those really easy video game monsters you fight at the very start of a game. Like a slime, an Eye Goo, or a Goblin from the Breath of Fire Series. Except the only wimpy monsters I can think of that are really recognizable are the slimes!

But that gives you small and easily digestible (I know some of the slimes had "flavors").

...maybe a weaker Pokemon.