What wasn't wrapped up from MGS3, admittedly I've never played Peace Walker (I have to wait until February 2012 for the HD collection European release)? Seriously enlighten me because I can't think of anything they missed.
I did however think of a loose end from MGS4, Doctor Madnar conveniently fixes Raiden & this is seemingly passed over in the story . I get a feeling from the new Rising trailer with all the cyborg enhancement flying about he's probably involved in some way.