Well maybe Aqua wasn't that close to him or maybe Xemnas doesn't remember her well enough. Sort of like a haze is over the memories (Riku about Sora).
...Wooo boy, I've come to the conclusion that you're die-hard of what you want to believe. Kinda makes me dizzy. @.@
Ok, here goes...When you go on an adventure to go and kill monsters and find some old and very powerful man, you'll get closer...And "friend" is a highly valued word in Kingdom Hearts, so it wouldn't have a light meaning on the level of "acquantance."
And all Sora had to remember was Kairi's name and all his memories starting flowing back. They didn't get connected automatically, but they all shone back into his heart...Not that they were out of it but...You get what I mean. And that Riku and Sora example isn't valid. Namine was screwing with everyone's memories, unintentionally, because Sora was regaining his own memories. Xemnas has no memory alteration brought on by an outside force.