Another nice little tidbit was posted on the Spider-Man Message Board in reference as to whether Trouble will become official Marvel cannon or note. Here's the quote:
I don't know if "Trouble" takes place in the Ultimate Universe. I'm pretty sure it doesn't take place in the Mainstream universe. I didn't see it my self, but someone on the http://www.joequesada.com site stated that Quesada has commented on this matter. The post said that Trouble hasn't been very well received and won't be part of the official Marvel canon. The poster also says that Millar has no plans to reference the story in his new title.
*phew* (the crowd sighs with relief)