Ask him how he'd feel about you naming one of them (if they were girls) completely after you, so she would be a female junior. I'm guessing he would laugh.
I personally don't like the idea of juniors, I find them sexist. My ex wanted to name our baby after him if it was a boy, but luckily we had a girl. Even if it had been a boy, I never would have budged. A middle name after family is fine, or even a first name after a more distant relative. But I could never do the junior thing, personally.
I don't think you should have to give up on your opinion just to avoid fighting with him - he needs to be able to compromise too. Your opinion counts just as much and after all YOU are the one sacrificing your body to give birth to these two babies. I also agree with you that it might be confusing/complicated for your kids if one of them has his name and the other doesn't. Even if they are opposite genders, the girl might wonder why she isn't named after you? Stick to your guns, that's my opinion.