I really liked the Magic Pickle series by Scott Morse as a kid (though trying to search it online at the time just led to a Harry Partridge animation) but I haven't read the new one that came out last year which went back to being a straight-forward comic.
I honestly dig middle grade comic from creators who have roots in the small-publisher/self-published scene.
Jimmy Gownley and Raina Telgemeier being examples themselves