What makes something charming and whimsical?
First you have to remember that action is the vehicle that moves the story along; it's the characters that make the ride enjoyable/interesting for your readers. 
I think the biggest thing that makes a story charming is strong characterization. Definitely like others have said, get to know your characters! Like really get to know them, not just their name. Consider their personalities and how they respond to certain situations.
I'm personally a big fan of defamiliarisation (glad there's a word for it, @wumblebumarts) and I plan on using it in my webcomic. Adding a quirk or unusual detail and passing it off as "the norm" is a great way to keep the readers entertained, and to make your job as the creator pretty fun too!! 
Examples:
ANIMAL CROSSING (You're the only human in a world of talking animals.)
SPACE JAM (Cartoons are real and live in an alternate dimension... it makes perfect sense, right?)
FOSTER HOME FOR IMAGINARY FRIENDS (Name says it all.)
So tl;dr, understand your characters, and give your story a quirky edge. When paired with a strong plot, you'll get a really great story.
Good luck! 