I have been developing a story and characters over the past few years. I plan on creating a novel that is very bizarre and gives an explanation for many of the unexplainable things that make society question the origins of. Basically the story is Fantasy but I plan on blending the time-line of my story to ours here on Earth. My primary Villain is not to be revealed till the second book which is a prequel to the first. He is a master manipulator and controls almost everything that happens in the story line including the villain in the first book. My question is how do I make a villain liked by the audience in the first book but at the same time hint the darkness within? I already have several characters not trusting this person in my story line and they call him out, even threaten him. I also have moments arise like when he is first introduced when he acts like is being attacked, but really was meeting up in secret with his would be attackers. But is that simple enough? Maybe I am over-thinking the whole thing I really don't know... Who is RJK?
If you want him to be liked by the reader, then try to treat him yourself as just another supporting character in the book. Try to forget that he is a villain for a while, and just concentrating on blending him in like any other character. I think readers can really get behind those characters getting picked on, so try to appeal to that by making us feel sympathy for him being threatened and 'wrongly' accused all the time.
The issue isn't with making him look wounded or attacked and bullied, I understand that concept. It's the moments when he is in a strange place or doing something that can be considered as suspicious in one way or another... How do I make it happen but not too obviously to the reader?
The trope for this type of villain is "the magnificent bastard". You can read more than you've ever cared to know about this trope here! http://tvtropes.org/pmwiki/pmwiki.php/Main/MagnificentBastard As with any character, the way you make him liked by the audience is to make him have traits that readers WISH they could have. Make him charismatic, make him hilarious, make him so unbelievably charming that the reader has no choice but to admire him. Even if he's truly the most evil person on the face of the earth, give him traits that the normal everyday person wishes they had, or had the chance to use more often. The ones that pop into my mind are charisma, affability, charm, and intelligence. Good luck!