So yes, they are going to be going up against organizations that may want super powered individuals or recover some super science or alien devices but with the exception of maybe RDJ looking over FitzSimmons' notes on something I doubt we'll see anyone (OK, maybe they run into Darcy, except she's on another network) from any of the movie franchises or any hero/villain that they may want to use in a movie franchise.
See, that's the problem. that idea starts to run thin pretty quickly. It's also why a lot of people, myself included, gave up on Alphas. When you have a show which is ostensibly about superheroes and the people that surround them, you expect to see them doing super things. Right now this show is treading a dangerous line of being too glib and cheeky, with very little pay off on the promise of "the agents of shield" living up to that vaunted organization. for instance, it was rather strongly alluded that the geegaw from episode 2 was nazi/hydra technology which had somehow been sent back in time 1500 years. yet I highly doubt that we're going to get a payoff on time travel because that would be too "super " for the show as it's been progressing thus far. it's POSSIBLE it was a tease for Cap2, but unlikely since that movie is not set in WWII either.
It's akin to tuning in to a show about the Navy SEALS, and watching them do nothing but paperwork and laundry all day long while talking about the cool stuff they do when you're not looking. pretty soon the joke wears thin.
As others have said, this show needs a consistent antagonist if it's going to keep going along, because they're not really executing "crisis of the week" very well at this point. at least IMhO.