I think Allison Susan just doesn't flow well--the ending sounds are too similar. I'd go with Susannah. (I'm also not a big believer that you "have" to be identical to honor someone--I think it's an honor that a name is inspired by the person you're honoring.)
Re: Middle Name
Not an option up there, but I like Allison Sue best!
I think anywhich way you want to honor someone is perfectly fine, if it counts and has meaning for you, it should count for the rest of us as well
Didn't even think of Sue - thanks!