Thank you for this site. It's amazing.
I created several characters, some of which are archetypal: mad-genius, flighty philosopher and so on.
Is it right to make the characters completely archetypal with physical characteristics according to the archetype or not?
For instance genius bit curly hair, an aquiline nose, body tall and thin? (As Sherlock Holmes). Will it make the novel less interesting because the characters are inherently recognizable and familiar?
Will it be confusing if the characters are opposite the archetypes?
I think what you are working with are what I might call stock characters rather than archetypes.
(For instance, if we consider protagonist and antagonist to be archetypal roles, then a mad genius could take on either of those roles in a story. Stock characters are about the external traits and personality types. Archetypal characters are about the dramatic roles certain characters play.)
The trouble with stock characters is that they are too recognizable. They don't seem authentic because they are based on characters from other stories rather than people in real life, so they seem derivative and cliched.
One thing you can do with a stock character to make it seem fresh is to play against the type. As you suggest, you can give them traits that seem to work at odds with the expectations and then figure out how to reconcile any apparent contradictions in a way that makes sense.
But even if you don't play with the external traits, the best thing you can do with stock characters is to give them authenticity and depth. Give the character an inner life with believable motivations, feelings, thoughts, goals, flaws, etc. Try to base the character more on real people than on fictional characters.
For instance, you might imagine what someone you know would be like if they were put in the position of the villain. What would it take to make them behave that way? How would they approach the problems they face, given their unique personality?
If your story is more plot-driven than character-driven, you may not want to take a lot of time describing each character's inner life. But look for places where you can add telling details that hint at what might be going on under the surface. Make sure the character reacts not just to what's happening externally but also in a way that reflects their unique personality and concerns.
Best of luck.