For starters, yes this is common. The majority of women have inner labia that protrude past the outer labia in some way. Only in the prepubescent category are slits more common than flowers.
In all the surveys I have seen, of the guys that care one way or the other, the vast majority prefer flowers over slits. You also have the group in the middle that would love to spend time with your labia. So if you actually want to have sex with him go ahead and do it. If he is one of the few guy that would run away from a nice pair of labia, then he isn't worth your anyway.
Be proud of what you have. Go enjoy yourself and stop worrying about what he might think!
I have never had a conversation with any of my friends that have turned into horror stories about a big inner labia. (Yes I know what your talking about, I took anatomy in HS) I wouldn't worry about it. If you think it really is a problem, talk to him about it. If he's a guy you want to be with he shouldn't really care but if he does then lose him and move on.
I have long inner labia that protrude beyond my labia majora. I have never had a guy say anything negative about my vulva. I used to be self-conscious about them because I didn't see many other girls that looked like me, but I got over it. From my experience guys could care less one way or the other they are just happy to have the privilege to be between your legs in the first place. Some guys have said they like performing oral sex on girls with larger labia more because there is more to pleasure and play with.