I imagine there are other SHIELD teams as well as rival agencies. Hydra, perhaps, could make for a good recurring villain.
Given that IM3 introduced A.I.M., I'm hoping it will be a recurring presence in future productions and eventually have its ties to HYDRA revealed. Although that would probably best be done in Cap 3 as a way of bringing the Red Skull back.
Well, no mention of Hydra in The Wolverine
. Not that that was hard to predict or anything, but I had wondered if it was going to be one of those elements that could be referenced by either franchise.