OK, I just felt like putting this out there, not that this "theory" (if you could even call it that) is going to happen or anything. I've noticed some apparent connections with Rayquaza (still obvious that it won't be the 3rd mascot though):
Firstly, Rayquaza is a trio master, and the 3rd mascot of the 3rd generation. This gen's 3rd legendary will also probably be a trio master. Secondly, people are assuming that there will be a R/S remake in this generation. Thirdly, many also believe that these games will have some sort of sky theme - Rayquaza is the sky guardian. Finally, rumours (although they may still be fake) claim that the 3rd legendary looks like a green snake - yep, Rayquaza says 'Hi'! There may be more "links" but I just wanted to share some interesting facts.