Not in any particular order of importance:
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Maria Hill (Cobie Smulders)
Ideally I'd like to see Maria Hill as a major recurring character (or, well, among the main cast), but Coulson getting the Director of S.H.I.E.L.D. promotion has somewhat diminished my hopes. Working at Stark Industries she could have been the channel for Coulson's rogue team to get resources and intel... but with their new secret Playground base do they really need her? And what does she think of Coulson getting promoted? I kinda think she won't be too happy...
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Glenn Talbot (Adrian Pasdar)
Adrian Pasdar's role this season was just a cameo, really, but hopefully that's a sign of more to come. Certainly Talbot shouldn't be done with Coulson yet. Especially Director Coulson! It will be quite some time before the military considers S.H.I.E.L.D. as trustworthy. I expect this to be a somewhat major part of the early season.
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Akela Amador (Pascale Armand)
Akela Amador was Coulson's former protégé and our introduction to advanced eye camera technology. She could still be a formidable ally in time of need.
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Felix Blake (Titus Welliver)
Agent Blake is the most prominently featured S.H.I.E.L.D. field agent outside of Coulson's team who is still alive (presumably). He's not exactly the most interesting character per se, but sooner or later Director Coulson has to try to make contact with surviving agents, no?
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Anne Weaver (Christine Adams)
That would be the headmaster of the S.H.I.E.L.D. Academy of Science and Technology from episode "Seeds", if the name doesn't ring any bells. Like Agent Blake, she seems like a logical person for Coulson's team to seek out, especially as she could be of use in Fitz's case. Last we heard of Weaver was in "Turn, Turn, Turn" during the HYDRA takeover. Her penultimate words to Simmons (before "Don't trust anyone!") were "If you survive, you know where to find me." Then there seemed to be some sort of explosion, true, but I believe she survived and those words she said to Simmons didn't just mean like "here in the Academy" but instead some specific hiding place or safehouse.
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Donnie Gill / Blizzard (Dylan Minnette)
He's got his cool superpowers, but it's yet to be seen how does he feel about them. I think it might still take him an episode or two to get to the whole supervillain Blizzard mode. Reform might follow in like season 3.
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Dr. Franklin Hall / Graviton (Ian Hart)
Dr. Franklin Hall was absorbed into the Gravitonium ball way back in episode 3, "The Asset". He hasn't been seen since, but the ball has changed hands into Ian Quinn's unreliable custody, so it seems inevitable that Graviton will soon be at large. Only question is, how large? I don't think he's Big Bad caliber, but he doesn't strike as lackey material either. After the long wait would it be too anticlimatic if he was just a "monster of the week"?
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Audrey Nathan (Amy Acker)
Is Phil ready to profess that he's not dead? If not, what else could draw the team to Portland, Oregon? I don't think Marcus Daniels /Blackout can carry another episode, it would be too similar to the last time (and the one before).
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Melinda May's as-of-yet unnamed mother (Tsai Chin)
Who is she and what agency did she work for before retiring? Flashbacks or not I'm sure we will learn much more of the background of the main characters in season 2. And we will meet May's mother again, no doubt.
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Elliot Randolph (Peter MacNicol)
For a number of reasons I think that "The Well" was one of the worst episodes of the first season, but Elliot Randoplh, a lowly Asgardian living on Earth, might still be worth visiting again. There will be no solo Thor movie during the second season, which might be all the more reason to remind the watchers that Asgard is still out there. Lady Sif and Lorelei, as great as they were, would be hard to use again (at least this soon) without it being too repetitive. Randolph on the other hand is more of a wildcard − and expendable. Wouldn't Raina be interested in tracking him down and dissecting him?
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Nick Fury (Samuel L. Jackson)
Fury has passed the torch to Director Coulson and slipped into the shadows, so it might take a while before we see him again. But my guess is that he'll show up before the second season is over, unless they get the season's worth of other cinematic guest stars.
...does
Stan Lee count as a character?