I hope that Athrun and Cagalli can be together, but even if they can't, I think that he'll be happy with Meyrin too. Meyrin and Cagalli are both such nice people, I wish they could both get the guy they want. T_T They both deserve happiness. I hope that whoever loses out on that love triangle finds someone else who makes them happy.
A Dearka/Miriallia reunion would b e wonderful. There'll definitely be Kira/Lacus, that's practically a given. XD I'd also like to see a resolution of Shinn's feelings for Stellar vs Lunamaria - does he really love Luna as more than a dear friend, or were they just grieving for Stellar and Meyrin when they got together? More Mwu/Murrue would be good - I'd like to see Mwu and Andy talking, too. I felt bad for him, he still misses Aisha.
It's not pairing-wise in any way, but I'd also really like to see Shinn and Cagalli have a discussion that doesn't end in yelling or crying. They have a lot more common ground than Shinn realises, and they both grew up through the series. I also agree with Murrue seeing Talia's son. I'd love to see even just a one-minute scene of Mwu reflecting on Auel, Sting and Stellar, and his time spent as Neo. Mwu himself is a good person, but Neo definitely wasn't - it seemed weird to me how he snapped from bad guy to good guy so seamlessly. Doesn't he feel bad about all the things he did as Neo?
I just really hope that like someone else said, there's not many/any new characters. The SEED/Destiny cast is big enough as it is - I'd rather see a movie that focuses on a new path for Kira, Lacus, Cagalli, Athrun, Shinn, the Hawke sisters, Yzak, Dearka, Mwu and Murrue (huge cast @_@) than a whole lot of newbies. If it were going to be a miniseries or multiple movies, sure, but one movie isn't enough time. I hope that it ends with a clear resolution, and most of all, no character deaths! It would be sad to get this far only for one of the main characters to die.