Adam Warlock/Magus
I get that the first film is centering on the core team. That said, there are so many cool members from the comic to adapt for the big screen. I think the most glarringly obvious misfire is that there's no Adam Warlock, or his counterpart, the evil Magus. I have no doubt that there will be rumblings of Magus throughout the movie. Then perhaps in the second movie he's partially an antagonist but reverts to Adam Warlock and joins the Guardians. Still, I think that we as fans of the comics would be saddened if Marvel completely overlooked this character.
Phylla-Vell
Another omission from the comics is Phylla-Vell, AKA Quasar or Martyr. She is very powerful and with the Quantum Bands she's a very cool part of Guardians and makes the team (in the comics) what they are. I think that her story ties in with that of Moondragon (more on that later) and to include the two in the sequel would make for an interesting story.
Richard Rider
I find it weird that we're getting the Nova Corps and no Nova. What's with that? Will Richard Rider appear in GOTG, or it's sequel? I think it's possible!
The Cancerverse
A rift in time and space opens up a portal to another dimension. This dimension is one where death doesn't exist, and the dimension is overpopulated. It's a grotesque version of the MArvel universe we know and love, and see it would be really cool for Marvel fans to see variation on many Marvel characters.
Moondragon
In the comics, Drax and Phylla-Vell teack down the daughter of Arthur Douglas (Drax) who was taken by Thanos and turned into Moondragon as we know her. A fierce telepath, her inclusion would make a Guardians sequel that much better!
Jack Flag
In the movie, I'd love to see Jack escape with the Guardians, and then perhaps near the end of the movie his spine is repaired. Leaving him an active member for the sequel.
Cosmo
Woof?