At first my protagonist was going to be a female role, until I started having an inclination for male characters and the fact that I am a total BL (“boy’s love”, stories about male homosexual romance) lover. So, I decided to make my character's gender up to the reader to decide since I know some people have different tastes in orientation. But it is much more difficult, since it is a visual novel. Any tips?
So I assume you aren't a well-established author, and people don't have preconceptions about how you will write. Obviously, you'll want to use gender-neutral names (like Terry) or establish them as nick-names (Bobby as a girl, for example).
Don't use pronouns. It will be a little weird, but in most situations, you keep gender out of it. Use short names and it might sound and flow better.
Make up pronouns. Everyone is shwa. A few years ago, I'd have said you couldn't get away with it, but I think readers today would be willing to go with it. You'll need to be explicit about keeping gender-types separate in a conversation, but it would be no different than using pronouns in a conversation between two people of the same gender. Be up front about it, and have a preface that states shwa is a universal pronoun. Most folks will assume you're just really PC, but the true agenda is secrecy.
If you want gender, but want it secret, you could go with shehe and heshe as pronouns. That way, everyone recognizes what people are relative to each other, but aren't clear which you're discussing (so you can tell cis/trans but not which is which).
Be ambiguous. If it's a visual novel, everyone wears ambiguous clothes and has the same haircut. Or a set variety of haircuts. Be - well - DODGY about it. Smart readers will quickly pick up on what you're doing, and they'll either rebel (in which case, they aren't you demographic anyway) or see it for what it is and appreciate it. In fact, they'd be disappointed if you DID reveal gender after making a point not to.
Some television series have characters which play an important role but are never shown, for example Wolowitz's mom in the "Big Bang Theory" or the wife of Niles in "Frasier". Maybe you could do the same with your protagonist in your comic/visual novel. Combine this with an unisex name and you are done.